long_read_rna_seq_analysis.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "P5k_WL74Y2Ei"
      },
      "source": [
        "#$\\text{L-RAPiT: Long Read Analysis Pipeline for Transcriptomics}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "IaygDNNEZnph"
      },
      "source": [
        "$\\text{A pipeline to analyze Oxford Nanopore and PacBio third-generation long transcriptomic sequencing reads}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "hIjUpSQCZlw1"
      },
      "source": [
        "$\\text{Theodore Nelson}$\n",
        "\n",
        "$\\text{Columbia University Irving Medical Center}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "_bUDAXz-7KYw"
      },
      "source": [
        "![flowchart.svg](data:image/svg+xml;base64,<?xml version="1.0" encoding="UTF-8"?>
<!-- Do not edit this file with editors other than diagrams.net -->
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<svg xmlns="http://www.w3.org/2000/svg" style="background-color: rgb(255, 255, 255);" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1" width="521px" height="881px" viewBox="-0.5 -0.5 521 881" content="&lt;mxfile host=&quot;app.diagrams.net&quot; modified=&quot;2022-12-07T05:46:03.218Z&quot; agent=&quot;5.0 (Macintosh)&quot; etag=&quot;aMM4CVCY6S2ialz-y0PR&quot; version=&quot;20.6.0&quot; type=&quot;google&quot;&gt;&lt;diagram id=&quot;C5RBs43oDa-KdzZeNtuy&quot; name=&quot;Page-1&quot;&gt;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&lt;/diagram&gt;&lt;/mxfile&gt;"><defs><style type="text/css">@import url(https://fonts.googleapis.com/css?family=Arial);&#xa;</style></defs><g><path d="M 260 320 L 260 343.63" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 260 348.88 L 256.5 341.88 L 260 343.63 L 263.5 341.88 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><path d="M 270 -170 L 265 -170 Q 260 -170 260 -160 L 260 80 Q 260 90 255 90 L 252.5 90 Q 250 90 255 90 L 257.5 90 Q 260 90 260 100 L 260 340 Q 260 350 265 350 L 270 350" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" transform="rotate(90,260,90)" pointer-events="all"/><path d="M 120 160 L 193.63 160" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 198.88 160 L 191.88 163.5 L 193.63 160 L 191.88 156.5 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><path d="M 400 160 L 326.37 160" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 321.12 160 L 328.12 156.5 L 326.37 160 L 328.12 163.5 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><path d="M 290 180 L 364.47 222.55" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 369.03 225.16 L 361.22 224.73 L 364.47 222.55 L 364.69 218.65 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><path d="M 230 180 L 155.7 217.15" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 151 219.5 L 155.7 213.24 L 155.7 217.15 L 158.83 219.5 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><path d="M 270 530 L 265 530 Q 260 530 260 540 L 260 780 Q 260 790 255 790 L 252.5 790 Q 250 790 255 790 L 257.5 790 Q 260 790 260 800 L 260 1040 Q 260 1050 265 1050 L 270 1050" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" transform="rotate(-90,260,790)" pointer-events="all"/><rect x="200" y="0" width="120" height="80" rx="12" ry="12" fill="#eff5fe" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 40px; margin-left: 201px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font style="font-size: 14px;" data-font-src="https://fonts.googleapis.com/css?family=Arial" face="Arial"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;"><b>Bioconda</b></font></font></div><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Install Programs</font></div></div></div></foreignObject><text x="260" y="44" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">BiocondaInstall Prog...</text></switch></g><rect x="370" y="120" width="120" height="80" rx="12" ry="12" fill="#fef6d8" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 160px; margin-left: 371px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font style="font-size: 14px;" data-font-src="https://fonts.googleapis.com/css?family=Arial" face="Arial">Upload <br /></font></div><div style="font-size: 14px;"><font style="font-size: 14px;" data-font-src="https://fonts.googleapis.com/css?family=Arial" face="Arial">Reads to <br /></font></div><div style="font-size: 14px;"><font style="font-size: 14px;" data-font-src="https://fonts.googleapis.com/css?family=Arial" face="Arial"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;">Google Drive</font><br /></font></div></div></div></div></foreignObject><text x="430" y="164" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">Upload...</text></switch></g><rect x="30" y="120" width="120" height="80" rx="12" ry="12" fill="#fef6d8" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 160px; margin-left: 31px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>Kingfisher</b><br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Download <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Public Data</font><br /></div></div></div></div></foreignObject><text x="90" y="164" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">Kingfisher...</text></switch></g><rect x="200" y="120" width="120" height="80" rx="12" ry="12" fill="#ffffff" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 160px; margin-left: 201px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><font style="font-size: 14px;" data-font-src="https://fonts.googleapis.com/css?family=Arial" face="Arial">Input Reads</font></div></div></div></foreignObject><text x="260" y="164" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">Input Reads</text></switch></g><rect x="30" y="220" width="120" height="80" rx="12" ry="12" fill="#f8ebff" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 260px; margin-left: 31px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>Shark</b><br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Filter Reads</font><br /></div></div></div></div></foreignObject><text x="90" y="264" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">Shark...</text></switch></g><rect x="370" y="220" width="120" height="80" rx="12" ry="12" fill="#eefeeb" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 260px; margin-left: 371px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>FastQC</b> <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Read Quality</font><br /></div></div></div></div></foreignObject><text x="430" y="264" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">FastQC...</text></switch></g><rect x="200" y="240" width="120" height="80" rx="12" ry="12" fill="#eff5fe" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 280px; margin-left: 201px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>minimap2</b><br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Align Reads</font></div></div></div></div></foreignObject><text x="260" y="284" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">minimap2...</text></switch></g><path d="M 260 200 L 260 233.63" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 260 238.88 L 256.5 231.88 L 260 233.63 L 263.5 231.88 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><path d="M 150 260 L 194.09 277.63" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 198.96 279.58 L 191.16 280.23 L 194.09 277.63 L 193.76 273.74 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><path d="M 200 390 L 180 390 L 180 610 L 180 720" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><rect x="200" y="350" width="120" height="80" rx="12" ry="12" fill="#eff5fe" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 390px; margin-left: 201px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>samtools</b> <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><font style="font-size: 14px;">Compress Alignments</font><br /></font></div></div></div></div></foreignObject><text x="260" y="394" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">samtools...</text></switch></g><rect x="370" y="350" width="120" height="80" rx="12" ry="12" fill="#eefeeb" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 390px; margin-left: 371px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>pistis</b><br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Alignment <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Quality</font><br /></div></div></div></div></foreignObject><text x="430" y="394" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">pistis...</text></switch></g><rect x="30" y="680" width="120" height="80" rx="12" ry="12" fill="#fef6d8" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 720px; margin-left: 31px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>TranscriptClean</b> <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Polish <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Alignments</font><br /></div></div></div></div></foreignObject><text x="90" y="724" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">TranscriptClean...</text></switch></g><rect x="30" y="350" width="120" height="80" rx="12" ry="12" fill="#f8e8e7" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 390px; margin-left: 31px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>svist4get</b> <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Graph <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Gene Coverage</font><br /></div></div></div></div></foreignObject><text x="90" y="394" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">svist4get...</text></switch></g><path d="M 180 390 L 156.37 390" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 151.12 390 L 158.12 386.5 L 156.37 390 L 158.12 393.5 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><rect x="30" y="460" width="120" height="80" rx="12" ry="12" fill="#f8e8e7" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 500px; margin-left: 31px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>MakeHub</b> <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Generate an<br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Alignment </font><font face="Arial">Viewer</font><br /></div></div></div></div></foreignObject><text x="90" y="504" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">MakeHub...</text></switch></g><rect x="200" y="460" width="120" height="80" rx="12" ry="12" fill="#fef6d8" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 500px; margin-left: 201px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>StringTie</b><br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Collapse<br /></font></div><div style="font-size: 14px;"><font face="Arial">Alignments</font><br /></div></div></div></div></foreignObject><text x="260" y="504" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">StringTie...</text></switch></g><path d="M 180 500 L 156.37 500" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 151.12 500 L 158.12 496.5 L 156.37 500 L 158.12 503.5 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><rect x="200" y="570" width="120" height="80" rx="12" ry="12" fill="#fef6d8" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 610px; margin-left: 201px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>GffCompare</b><br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Cross-Reference</font></div><div style="font-size: 14px;">Collapsed Alignments<br /></div></div></div></div></foreignObject><text x="260" y="614" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">GffCompare...</text></switch></g><path d="M 260 540 L 260 563.63" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 260 568.88 L 256.5 561.88 L 260 563.63 L 263.5 561.88 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><rect x="370" y="460" width="120" height="80" rx="12" ry="12" fill="#fef6d8" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 500px; margin-left: 371px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>featureCounts</b> <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Produce <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Gene Counts<br /></font></div></div></div></div></foreignObject><text x="430" y="504" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">featureCounts...</text></switch></g><rect x="370" y="570" width="120" height="80" rx="12" ry="12" fill="#fef6d8" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 610px; margin-left: 371px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>LIQA</b> <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Produce <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Transcript Counts<br /></font></div></div></div></div></foreignObject><text x="430" y="614" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">LIQA...</text></switch></g><rect x="370" y="680" width="120" height="80" rx="12" ry="12" fill="#f8ebff" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 720px; margin-left: 371px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>FLAME</b> <br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Predict Novel Splicing Events<br /></font></div></div></div></div></foreignObject><text x="430" y="724" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">FLAME...</text></switch></g><rect x="200" y="800" width="120" height="80" rx="12" ry="12" fill="#eefeeb" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 840px; margin-left: 201px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>MultiQC</b>: <br /></font></div><div><font style="font-size: 14px;" data-font-src="https://fonts.googleapis.com/css?family=Arial" face="Arial">Compile <br /></font></div><div><font style="font-size: 14px;" data-font-src="https://fonts.googleapis.com/css?family=Arial" face="Arial">Statistics</font></div></div></div></div></foreignObject><text x="260" y="844" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">MultiQC:...</text></switch></g><path d="M 320 390 L 340 390 L 340 610 L 340 720" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 340 390 L 363.63 390" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 368.88 390 L 361.88 393.5 L 363.63 390 L 361.88 386.5 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><path d="M 340 499.5 L 363.63 499.5" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 368.88 499.5 L 361.88 503 L 363.63 499.5 L 361.88 496 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><path d="M 340 609.77 L 363.63 609.77" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 368.88 609.77 L 361.88 613.27 L 363.63 609.77 L 361.88 606.27 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><path d="M 340 719.77 L 363.63 719.77" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 368.88 719.77 L 361.88 723.27 L 363.63 719.77 L 361.88 716.27 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><rect x="30" y="570" width="120" height="80" rx="12" ry="12" fill="#fef6d8" stroke="rgb(0, 0, 0)" pointer-events="all"/><g transform="translate(-0.5 -0.5)"><switch><foreignObject style="overflow: visible; text-align: left;" pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"><div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 610px; margin-left: 31px;"><div style="box-sizing: border-box; font-size: 0px; text-align: center;" data-drawio-colors="color: rgb(0, 0, 0); "><div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;"><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial"><b>FusionSeeker</b><br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Identify<br /></font></div><div style="font-size: 14px;"><font data-font-src="https://fonts.googleapis.com/css?family=Arial" style="font-size: 14px;" face="Arial">Gene Fusions<br /></font></div></div></div></div></foreignObject><text x="90" y="614" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">FusionSeeker...</text></switch></g><path d="M 181 610 L 157.37 610" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 152.12 610 L 159.12 606.5 L 157.37 610 L 159.12 613.5 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><path d="M 180 720 L 156.37 720" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 151.12 720 L 158.12 716.5 L 156.37 720 L 158.12 723.5 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/><path d="M 260 430 L 260 453.63" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/><path d="M 260 458.88 L 256.5 451.88 L 260 453.63 L 263.5 451.88 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/></g><switch><g requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"/><a transform="translate(0,-5)" xlink:href="https://www.diagrams.net/doc/faq/svg-export-text-problems" target="_blank"><text text-anchor="middle" font-size="10px" x="50%" y="100%">Text is not SVG - cannot display</text></a></switch></svg>)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "AUKHTlobUcf_"
      },
      "source": [
        "##$\\color{#e74b4b}{\\text{Parameter Input and User Instructions}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "oM-NaZDK63YC"
      },
      "source": [
        "Please define where the file structure is within your Google Drive:"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "uc1rzY2x6tvu"
      },
      "source": [
        "<ul type=disc>\n",
        "<li><b>PIPELINE_FILE_PATH</b>: file path to location of long-read RNA sequencing analysis pipeline within your Google Colab/Google Drive/local file system - required for most applications. This must be defined and initialized first.</li>\n",
        "</ul>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "cviQcgv7iqvo"
      },
      "source": [
        "Please note: when utilizing the default ```/content``` location on a colab machine, click on the folder icon (fourth icon from the top on the left menu) to see files listed in a graphical user interface.  "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "_P4OAFNrzifE"
      },
      "outputs": [],
      "source": [
        "%env PIPELINE_FILE_PATH=/content"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "_GxZ1UCRTDkt"
      },
      "source": [
        "Errors associated with the following command are most likely associated with the existence of the directory/folder where the pipeline will be installed. "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "Hpn2CRCkJTfT"
      },
      "outputs": [],
      "source": [
        "! mkdir $PIPELINE_FILE_PATH"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "I24mo0O8JF4P"
      },
      "outputs": [],
      "source": [
        "! cd $PIPELINE_FILE_PATH ; git clone https://github.com/Theo-Nelson/long-read-sequencing-pipeline"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "2USxlBU47A0L"
      },
      "source": [
        "Please modify the following parameters within the code box below to fit your own study requirements:  "
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "f99vaAE0Z0AG"
      },
      "source": [
        "<li><b>ACC</b>: Run accession number for reads within the [European Nucleotide Archive](https://www.ebi.ac.uk/ena/browser/) (SRR...) or file path to location of long-read RNA sequencing data within your Google Drive/general file system - required for most applications</li>\n",
        "<li><b>INDEX_FILE_PATH</b>: file path to location of reference genome (e.g. .FASTA) within your Google Drive/general file system - required for most applications</li>\n",
        "<li><b>ANNOTATION_FILE_PATH</b>: file path to location of reference annotation (e.g. .GTF) within your Google Drive/general file system - required for most applications</li>\n",
        "<li><b>CHROMOSOME</b>: Name of Chromosome of Interest matching the name of the Chromosome within your Reference Annotation - required for svist4get</li>\n",
        "<li><b>CHROMOSOME_START</b>: Starting Location of Interest on the Chromosome - required for svist4get</li>\n",
        "<li><b>CHROMOSOME_FINISH</b>: Ending Location of Interest on the Chromosome - required for svist4get</li>\n",
        "<li><b>REGION_NAME</b>: Gene Name (should match annotation file) - required for FLAME and svist4get</li>\n",
        "<li><b>HUB_KEYWORD</b>: Short Keyword for your UCSC Track Hub - required for MakeHub</li>\n",
        "<li><b>HUB_NAME</b>: Longer Title for your UCSC Track Hub - required for MakeHub</li>\n",
        "<li><b>HUB_EMAIL</b>: Email for your UCSC Track Hub (if you publish your track hub then this email will be public) - required for MakeHub</li>\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "tqGM1OFhUcoo"
      },
      "outputs": [],
      "source": [
        "%env ACC=DRR059311\n",
        "%env INDEX_FILE_PATH=${PIPELINE_FILE_PATH}/long-read-sequencing-pipeline/prebuilt_indices/hg38.fa\n",
        "%env ANNOTATION_FILE_PATH=${PIPELINE_FILE_PATH}/long-read-sequencing-pipeline/prebuilt_indices/GCA_000001405.29_GRCh38.p14_genomic.gtf\n",
        "%env CHROMOSOME=chr12\n",
        "%env CHROMOSOME_START=116533422\n",
        "%env CHROMOSOME_FINISH=116536513\n",
        "%env REGION_NAME=LINC00173\n",
        "%env HUB_KEYWORD=LINC00173\n",
        "%env HUB_NAME=\"Human LINC00173\"\n",
        "%env HUB_EMAIL=your@email.address"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "RrTcAlHtbWfg"
      },
      "source": [
        "##$\\color{#e74b4b}{\\text{Mounting your Google Drive / Exporting to Your Local Hard Drive}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "C5_iJ_KkbYt3"
      },
      "source": [
        "This step allows for permanent storage of your bioinformatics analysis in Google Drive"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "rbS0P9JcJnnJ"
      },
      "source": [
        "<ul type=disc>\n",
        "<li><b>STORAGE_FILE_PATH</b>: file path to location where you would wish to store output of long-read RNA sequencing analysis pipeline - required to export data from Google Colab. </li>\n",
        "</ul>"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "igrdHc7NJ3Zr"
      },
      "outputs": [],
      "source": [
        "%env STORAGE_FILE_PATH=/content/drive/MyDrive/long-read-sequencing-pipeline"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "aQOezcA5ZrFA"
      },
      "outputs": [],
      "source": [
        "from google.colab import drive\n",
        "drive.mount('/content/drive')"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "e1fBbVvQgvYF"
      },
      "source": [
        "Errors associated with the following command are most likely associated with the existence of the directory/folder where the pipeline will be installed. "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "aqCDej0lgrX7"
      },
      "outputs": [],
      "source": [
        "! mkdir $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "fZaStpCheIm0"
      },
      "source": [
        "Additionally, this command will export necessary parameter data to allow downloads to a local machine. Please ignore ```/bin/bash: line 0: export: `/content': not a valid identifier``` or similar errors. "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "reOYVKmaeI81"
      },
      "outputs": [],
      "source": [
        "! export $ACC\n",
        "! export $PIPELINE_FILE_PATH\n",
        "! export $REGION_NAME"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "24vu4E_8vbKa"
      },
      "source": [
        "##$\\color{#e74b4b}{\\text{BioConda: Package Installations}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "lz3I3YU06E6z"
      },
      "source": [
        "BioConda is a software environment and package manager, providing acess to over 8,000 different software packages related to bioinformatics (documentation: [BioConda](https://bioconda.github.io/user/install.html) and [Managing Environments via Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)). "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "oxEPAO-_wpbz"
      },
      "outputs": [],
      "source": [
        "! wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh\n",
        "! chmod +x Miniconda3-py37_4.8.2-Linux-x86_64.sh\n",
        "! bash ./Miniconda3-py37_4.8.2-Linux-x86_64.sh -b -f -p /usr/local"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "EZS5nfFJCNHz"
      },
      "outputs": [],
      "source": [
        "! export PYTHONHOME='/usr/local/lib/python3.7/site-packages/'"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "z1lysGn4hO-i"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{Kingfisher: procurement of sequence files - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "X4iuuuqPkKcT"
      },
      "source": [
        "The Kingfisher program allows for sequence files to be downloaded from the European Nucleotide Archive (documentation: https://github.com/wwood/kingfisher-download)."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "l9lQPVf27Itd"
      },
      "outputs": [],
      "source": [
        "! conda create -n kingfisher -c conda-forge -c bioconda python=3.9 kingfisher -y"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "fDjCnO4C3NQu"
      },
      "outputs": [],
      "source": [
        "! conda install -c rpetit3 aspera-connect -y"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ksJvQOCtx8BJ"
      },
      "outputs": [],
      "source": [
        "! wget -qO- https://download.asperasoft.com/download/sw/connect/3.9.8/ibm-aspera-connect-3.9.8.176272-linux-g2.12-64.tar.gz | tar xvz"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "RHjWyX6Ei_jT"
      },
      "source": [
        "this command will pop up with an error message; please disregard"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "anXSgAYa3xQU"
      },
      "outputs": [],
      "source": [
        "! ./ibm-aspera-connect-3.9.8.176272-linux-g2.12-64.sh"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "F0hFNwmcv5qr"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{FastQC: quality control tool for high-throughput sequence data - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "68fqL9EGNOKE"
      },
      "source": [
        "FastQC is a program designed to spot potential problems in high througput sequencing datasets ([documentation](https://github.com/s-andrews/FastQC))."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "_bRfEf9e3Sp-"
      },
      "outputs": [],
      "source": [
        "! conda install -c bioconda fastqc -y"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "k_oe5__lB6Lz"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{Shark: fishing relevant reads in an RNA-Seq sample - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Pa8jDrcgB9xl"
      },
      "source": [
        "Shark is a tool to extract gene-specific reads from a RNA-seq sample (documentation: https://github.com/AlgoLab/shark)."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "PEjwM6_7B96Z"
      },
      "outputs": [],
      "source": [
        "! conda install -c bioconda shark -y"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "gyh52FxVTSQt"
      },
      "source": [
        "###$\\color{#e74b4b}{\\text{minimap2: A versatile pairwise aligner for spliced nucleotide sequences - installation}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "0bXGX4mEeegN"
      },
      "source": [
        "minimap2 is a long-read sequencing aligner (documentation: https://github.com/lh3/minimap2). "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "yZz8ktFYTQ1F"
      },
      "outputs": [],
      "source": [
        "! conda create -n minimap2 -c conda-forge -c bioconda minimap2=2.23 -y"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "dxspwFM3_1qN"
      },
      "source": [
        "###$\\color{#e74b4b}{\\text{samtools: Write/Index SAM to BAM - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "SXphSNhPA9di"
      },
      "source": [
        "samtools allows for manipulation of high-throughput sequencing data (documentation: http://www.htslib.org/) \n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "v0_UcWdBHDGQ"
      },
      "outputs": [],
      "source": [
        "! conda create -n samtools -c conda-forge -c bioconda python=3.7 samtools -y"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Y9qrP4Ip3xwz"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{TranscriptClean: correct mismatches, microindels, and noncanonical splice junctions - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "bB4Zr5Ef38qi"
      },
      "source": [
        "TranscriptClean is a command-line program which corrects long-read mismatches, microindels and noncanonical splice junctions (documentation: https://github.com/mortazavilab/TranscriptClean). "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "oXIztTkj3zbu"
      },
      "outputs": [],
      "source": [
        "! conda install -c bioconda pyfasta pyranges samtools -y"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "BfsI59QG4BH_"
      },
      "outputs": [],
      "source": [
        "! wget https://github.com/mortazavilab/TranscriptClean/archive/refs/tags/v2.0.3.tar.gz\n",
        "! tar xvf v2.0.3.tar.gz "
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "3U_BpHSJA9Xe"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{FLAME: long-read splice variant annotation - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "7_98iJtTy1wr"
      },
      "source": [
        "Full-Length Adjacency Matrix Enumeration (FLAME) is a program which can detect and quantify novel splice junctions on an annotated gene locus (documentation: https://github.com/marabouboy/FLAME). "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "cyzQjKxz7H1v"
      },
      "outputs": [],
      "source": [
        "! sudo apt-get install bedtools"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "rvgXztd99NMC"
      },
      "outputs": [],
      "source": [
        "! pip install pysam"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "pKvCCPWvBJ2b"
      },
      "outputs": [],
      "source": [
        "! git clone https://github.com/marabouboy/FLAME"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "TZaGFSOoVUCo"
      },
      "outputs": [],
      "source": [
        "! chmod 755 /content/FLAME/FLAME/FLAME.py"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "7Erq_G3QVlz9"
      },
      "outputs": [],
      "source": [
        "! chmod 755 /content/FLAME/setup.py"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "grBakyZXVv3s"
      },
      "outputs": [],
      "source": [
        "! cd /content/FLAME/ ; python3 setup.py install"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "yhR96h7O5CHN"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{featureCounts: assign sequence reads to genomic features - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "VnlTGqwG5JYz"
      },
      "source": [
        "featureCounts is a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments (documentation: http://subread.sourceforge.net/). "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "Vd48uWN45VkA"
      },
      "outputs": [],
      "source": [
        "! conda install -c bioconda subread -y"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "vZPSGeXlh7kh"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{LIQA: transcript quantification}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "vMq1SRmih_SS"
      },
      "source": [
        "LIQA is a program which quantifies isoform/transcript expression based on long read RNA sequencing data (documentation: https://github.com/WGLab/LIQA)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ggyRF2F953H8"
      },
      "outputs": [],
      "source": [
        "! pip install liqa"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "oOS4NvQ8o5Q7"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{FusionSeeker: detect gene fusions - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "mJKun3uw-Ihy"
      },
      "source": [
        "FussionCaller is a gene fusion caller for long-read single-molecular sequencing data (documentation: https://github.com/Maggi-Chen/FusionSeeker). "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "fvgPhbBwmkzP"
      },
      "outputs": [],
      "source": [
        "! git clone https://github.com/Theo-Nelson/FusionSeeker.git"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "bEPIzmwa2dFO"
      },
      "outputs": [],
      "source": [
        "! git clone https://github.com/ruanjue/bsalign.git"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "mlblnJtF2eyk"
      },
      "outputs": [],
      "source": [
        "! cd /content/bsalign && make"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "EFHE0ybf9rRI"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{StringTie: transcript assembly - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "WCeEyrb4S0xW"
      },
      "source": [
        "StringTie is a program which can produce transcriptomes specific to the sample input (documentation: http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#run)."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ljsRmfFksCki"
      },
      "outputs": [],
      "source": [
        "! conda install -c bioconda stringtie -y"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "CId-MKlu9uMZ"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{GffCompare: transcript assembly statistics - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Hy2ietg1UPWj"
      },
      "source": [
        "GffCompare is a program which can evaluate the specificity and novelty of transcripts within a sample-specific transcriptome to a reference transcriptome (documentation: http://ccb.jhu.edu/software/stringtie/gffcompare.shtml)."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "iKx4Bn4wSyLb"
      },
      "outputs": [],
      "source": [
        "! conda install -c bioconda gffcompare -y"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "npZwllsupfEJ"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{svist4get: visualize genomic tracks from sequencing experiments - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "niesqrQ1nHMM"
      },
      "source": [
        "svist4get allows you to view read coverage at a defined region on a chromosome (documentation: https://bitbucket.org/artegorov/svist4get/src/master/)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "iaRNkYPEoa0T"
      },
      "outputs": [],
      "source": [
        "! apt-get update"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "-gNi5jxXA5oq"
      },
      "outputs": [],
      "source": [
        "! apt-get install libmagickwand-dev"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "3HS96PJ45f26"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/svist4get/policy_revised.xml /etc/ImageMagick-6/policy.xml"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ZNVRJydu1wIV"
      },
      "outputs": [],
      "source": [
        "! python3 -m pip install svist4get"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "5CwywN4tc74s"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{Pistis: quality control plotting for long reads - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ckgZcyKcpFyC"
      },
      "source": [
        "Pistis generates long-read specific quality control graphs, including a plot demonstrating read alignment percentage to the reference genome (documentation: https://github.com/mbhall88/pistis)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "S5mHHUr1d50q"
      },
      "outputs": [],
      "source": [
        "! pip3 install pistis"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "EQn9Ikb3YkFC"
      },
      "source": [
        "###$\\color{#0072ff}{\\text{MakeHub: generate UCSC assembly hubs - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "X7J1qXU1bmXd"
      },
      "source": [
        "MakeHub is a command line tool for the fully automatic generation of of track data hubs for visualizing genomes with the UCSC genome browser (documentation: https://github.com/Gaius-Augustus/MakeHub)."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "_eYWwdsmdsBa"
      },
      "outputs": [],
      "source": [
        "! python3.7 -m pip install biopython"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "yudzuOTW2IQ-"
      },
      "outputs": [],
      "source": [
        "! sudo apt install augustus augustus-data augustus-doc"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "kpfzCCTKuqMt"
      },
      "source": [
        "###$\\color{#ff00d5}{\\text{MultiQC: aggregate bioinformatics analysis - installation}}$\n",
        "\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Jluk65BgNoEJ"
      },
      "source": [
        "MultiQC is a program which allows you to combine reports for as many samples as you wish ([documentation](https://multiqc.info/docs/))"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "B6OuaTChNs4J"
      },
      "outputs": [],
      "source": [
        "! pip install multiqc"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "oBdBA_CDdE0z"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{Kingfisher: procurement of sequence files - usage}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "IE4T9swGdQY-"
      },
      "source": [
        "The Kingfisher program allows for sequence files to be downloaded from the European Nucleotide Archive (documentation: https://github.com/wwood/kingfisher-download)."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ReZdoTfnd5uQ"
      },
      "outputs": [],
      "source": [
        "! cd $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastq ; source activate kingfisher ; kingfisher get -r $ACC -m ena-ascp aws-http prefetch"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "V5WMZKjYx6YU"
      },
      "source": [
        "The next command will unzip a fastq file, if neccessary. Please do not be concerned if this command throws an error. "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "wwpiZ9OU6WPn"
      },
      "outputs": [],
      "source": [
        "! cd $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastq ; gunzip *.gz"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "izrcNnG0REyD"
      },
      "source": [
        "The next two commands simply standardize the file name away from uncommon variants provided by depositors in the European Nucleotide Archive. In rare instances pipeline users may need to directly manipulate these commands to standardize the filename. Please do not be concerned if either command throws an error. "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "4pmkDR2x6SzT"
      },
      "outputs": [],
      "source": [
        "! cd $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastq ; mv ${ACC}_1.fastq $ACC.fastq"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "5_r7Ed86Q-cI"
      },
      "outputs": [],
      "source": [
        "! cd $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastq ; mv ${ACC}_subreads.fastq $ACC.fastq"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "_MislmkXZcz-"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{Kingfisher: procurement of sequence files - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "-mPcrcf-Kmfl"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "U0pvTRDjKtqG"
      },
      "outputs": [],
      "source": [
        "! eval cp $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastq/$ACC.fastq $STORAGE_FILE_PATH/$ACC.fastq"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "txLoObMrKrnJ"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "sWZhEEl3KuIu"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/fastq/\",os.path.expandvars(os.path.expandvars(\"$ACC\")),\".fastq\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "SQb5HTiwtfMn"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{FastQC: quality control tool for high-throughput sequence data - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ZoutKrvVtjAY"
      },
      "source": [
        "FastQC is a program designed to spot potential problems in high througput sequencing datasets ([documentation](https://github.com/s-andrews/FastQC))."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "bTYA5m273eVN"
      },
      "outputs": [],
      "source": [
        "! eval fastqc -t 2 $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastq/$ACC.fastq --outdir $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastqc"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "nHGHIAKCSUen"
      },
      "source": [
        "For the best viewing experience, please download the HTML output to your Hard Drive and open in your local browser, such as Google Chrome, Firefox or Edge. "
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "NOrgEp-fbtBt"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{FastQC: quality control tool for high-throughput sequence data - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "bGhAXFSfbtBx"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "z2dsXIK4btBy"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastqc/ $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "6CZoOeptbtB0"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "H3dCOerJqUoS"
      },
      "outputs": [],
      "source": [
        "! zip -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastqc.zip $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastqc/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "LqiW6frsbtB1"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/fastqc.zip\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "7uHwZ4Zj1vgC"
      },
      "source": [
        "##$\\color{#e74b4b}{\\text{Reference Genome - installation}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "5FvumDB7c6bH"
      },
      "source": [
        "The Reference Genome provides a scaffold to align long-read data. These commands install the hg38 genome and ensembl annotation availiable from UCSC. You can download more current genomes by utilizing the appropriate links from NCBI RefSeq, Ensembl, or other reference genome providers. If you are unsure of how to find other species, we recommend checking out the list of species available in the ```current_fasta``` and ```current_gtf``` folders: http://ftp.ensembl.org/pub/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "_D5cG18VURVJ"
      },
      "outputs": [],
      "source": [
        "! wget -P $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "Jy4bAiZ6z3Qb"
      },
      "outputs": [],
      "source": [
        "! wget -P $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.29_GRCh38.p14/GCA_000001405.29_GRCh38.p14_genomic.gtf.gz"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "bz8hNYEvUXOE"
      },
      "outputs": [],
      "source": [
        "! gunzip -c $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/hg38.fa.gz > $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/hg38.fa"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "z2Hqu_wb0NOv"
      },
      "outputs": [],
      "source": [
        "! gunzip -c $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/GCA_000001405.29_GRCh38.p14_genomic.gtf.gz > $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/GCA_000001405.29_GRCh38.p14_genomic.gtf"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "iulCArtGA6sw"
      },
      "source": [
        "Another example is provided for which installs the UCSC murine mm39 genome. Note that the reference annotation is from RefSeq. "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "rf6DUsMHBUmp"
      },
      "outputs": [],
      "source": [
        "! wget -P $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.9_GRCm39/GCA_000001635.9_GRCm39_genomic.fna.gz"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "IL949aPzBUsA"
      },
      "outputs": [],
      "source": [
        "! wget -P $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.9_GRCm39/GCA_000001635.9_GRCm39_genomic.gtf.gz"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "vAqaExDBBUxi"
      },
      "outputs": [],
      "source": [
        "! gunzip -c $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/GCA_000001635.9_GRCm39_genomic.fna.gz > $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/GCA_000001635.9_GRCm39_genomic.fa"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "suKULpveBU20"
      },
      "outputs": [],
      "source": [
        "! gunzip -c $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/GCA_000001635.9_GRCm39_genomic.gtf.gz > $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/GCA_000001635.9_GRCm39_genomic.gtf"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "D6iKV4YDiJQk"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{Shark: fishing relevant reads in an RNA-Seq sample - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "9BtvLo6dHRxt"
      },
      "source": [
        "Shark is a tool to extract gene-specific reads from a RNA-seq sample (documentation: https://github.com/AlgoLab/shark)."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "Jjx8LrclHVCH"
      },
      "outputs": [],
      "source": [
        "! echo ${CHROMOSOME}$'\\t'${CHROMOSOME_START}$'\\t'${CHROMOSOME_FINISH} > $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/$REGION_NAME.bed"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "BxccuEsbFpyJ"
      },
      "outputs": [],
      "source": [
        "! eval bedtools getfasta -fi $INDEX_FILE_PATH -bed $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/$REGION_NAME.bed -fo $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/$REGION_NAME.fasta"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "FB1MpOyLnRxD"
      },
      "outputs": [],
      "source": [
        "! eval shark -c .40 -k 10 -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/$REGION_NAME.fasta -1 $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastq/$ACC.fastq -o $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastq/$REGION_NAME$ACC.fastq"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "cDYzmwgwdZtX"
      },
      "source": [
        "In order to continue analysis with just the filtered reads, please utilize the following commands:"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "1uQp4_LvYtPi"
      },
      "outputs": [],
      "source": [
        "import os\n",
        "os.environ[\"ACC_cp\"] = os.environ[\"ACC\"]"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "mZGMFpxiRROC"
      },
      "outputs": [],
      "source": [
        "%env ACC = $REGION_NAME$ACC_cp"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "EJ0KI6ZxJInS"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{Shark: fishing relevant reads in an RNA-Seq sample - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Q3quwJI4JInW"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "11khL1RgJInX"
      },
      "outputs": [],
      "source": [
        "! eval cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastq/$REGION_NAME.fastq $STORAGE_FILE_PATH/$REGION_NAME$ACC.fastq"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ePctHvJkJInY"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "a1IIimzeJInb"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/fastq/\",os.environ[\"REGION_NAME\"],os.environ[\"ACC\"],\".fastq\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "oBPQyTcKOPDF"
      },
      "source": [
        "##$\\color{#e74b4b}{\\text{minimap2: A versatile pairwise aligner for spliced nucleotide sequences - index minimization}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "of339UK9OT_0"
      },
      "source": [
        "minimap2 is a long-read sequencing aligner (documentation: https://github.com/lh3/minimap2). "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ZFQz8s-vFrNG"
      },
      "outputs": [],
      "source": [
        "! source activate minimap2 ; eval minimap2 -I2G -k15 -w5 -d $INDEX_FILE_PATH.mmi $INDEX_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "f8EfwQZze29B"
      },
      "source": [
        "##$\\color{#e74b4b}{\\text{minimap2: A versatile pairwise aligner for spliced nucleotide sequences - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "xlj72R1ofOAz"
      },
      "source": [
        "minimap2 is a long-read sequencing aligner (documentation: https://github.com/lh3/minimap2). "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "YjPnVj5PTRtK"
      },
      "outputs": [],
      "source": [
        "! source activate minimap2 ; eval minimap2 --split-prefix -k15 -ax splice $INDEX_FILE_PATH.mmi $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastq/$ACC.fastq > $(eval echo $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/sam/$ACC.sam)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "J_OH_OItuBjO"
      },
      "source": [
        "##$\\color{#e74b4b}{\\text{minimap2: A versatile pairwise aligner for spliced nucleotide sequences - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "tCKOQBzbuBjR"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "xEM-Bg_nuBjS"
      },
      "outputs": [],
      "source": [
        "! eval cp $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/sam/$ACC.sam $STORAGE_FILE_PATH/$ACC.sam"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "sfmGI2VruBjS"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "zpy-NJKXuBjU"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/sam/\",os.path.expandvars(os.path.expandvars(\"$ACC\")),\".sam\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "sjns1XbAkILI"
      },
      "source": [
        "##$\\color{#e74b4b}{\\text{samtools: Write/Index SAM to BAM - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "KfgkJ0bJkYDv"
      },
      "source": [
        "samtools allows for manipulation of high-throughput sequencing data (documentation: http://www.htslib.org/) \n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "fAFTMfy2HDOs"
      },
      "outputs": [],
      "source": [
        "! source activate samtools ; eval samtools view -S -b $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/sam/$ACC.sam > $(eval echo $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.bam)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "qYOZbl8PJo-h"
      },
      "outputs": [],
      "source": [
        "! source activate samtools ; eval samtools sort $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.bam -o $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.sorted.bam  "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ypjDsfP7JpM6"
      },
      "outputs": [],
      "source": [
        "! source activate samtools ; eval samtools index $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.sorted.bam "
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "swcyphLAvE52"
      },
      "source": [
        "##$\\color{#e74b4b}{\\text{samtools: Write/Index SAM to BAM - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "GbZSSgbkvE54"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "qi5xpmLnvE55"
      },
      "outputs": [],
      "source": [
        "! eval cp $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.sorted.bam $STORAGE_FILE_PATH/$ACC.sorted.bam"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "_QPGPrNnXNi_"
      },
      "outputs": [],
      "source": [
        "! eval cp $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.sorted.bam.bai $STORAGE_FILE_PATH/$ACC.sorted.bam.bai"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "psCo62ZRvE57"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "TSjtffSHvE59"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/bam/\",os.path.expandvars(os.path.expandvars(\"$ACC\")),\".sorted.bam\"]))"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "sD5KruF8XV86"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/bam/\",os.path.expandvars(os.path.expandvars(\"$ACC\")),\".sorted.bam.bai\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "zqQcBdxa4X7q"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{TranscriptClean: correct mismatches, microindels, and noncanonical splice junctions - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "r5CNnQ5w4k_K"
      },
      "source": [
        "TranscriptClean is a command-line program which corrects long-read mismatches, microindels and noncanonical splice junctions (documentation: https://github.com/mortazavilab/TranscriptClean). "
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ZU_kVYSvWXdN"
      },
      "source": [
        "Please note that the corrected reads should not be utilized for downstream-level base-calling analysis such as variant calling. "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "sJPb4PSU5LmU"
      },
      "outputs": [],
      "source": [
        "! eval python /content/TranscriptClean-2.0.3/TranscriptClean.py --sam $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/sam/$ACC.sam --genome $INDEX_FILE_PATH --outprefix $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/transcriptclean/$ACC"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "11Qa37-tea-K"
      },
      "source": [
        "Convert the resulting sam file to a bam file:"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "bn_4YOoJd68N"
      },
      "outputs": [],
      "source": [
        "! eval samtools view -S -b $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/transcriptclean/$(eval echo $ACC)_clean.sam > $(eval echo $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$(eval echo $ACC)_clean.bam)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "kVdkAQw0eStU"
      },
      "outputs": [],
      "source": [
        "! eval samtools sort $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$(eval echo $ACC)_clean.bam -o $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$(eval echo $ACC)_clean.sorted.bam  "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "G8A4OL32eXcI"
      },
      "outputs": [],
      "source": [
        "! eval samtools index $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$(eval echo $ACC)_clean.sorted.bam "
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "iUwbIIRkwWrL"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{TranscriptClean: correct mismatches, microindels, and noncanonical splice junctions - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "1K-zlCYDwWrL"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "j_1xnKJJwWrM"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/transcriptclean/ $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "tcK1cY7pwWrN"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "_t5YZRckdd_T"
      },
      "outputs": [],
      "source": [
        "! zip -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/transcriptclean.zip $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/transcriptclean/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "RW7dqOgpwWrP"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/transcriptclean.zip\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "BKjT28HjsBkW"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{StringTie: transcript assembly - usage}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "FuoJtl20TNAx"
      },
      "source": [
        "StringTie is a program which can collapse sample reads into transcriptomes specific to the sample input (documentation: http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#run)."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "_gRdTG0lsDQb"
      },
      "outputs": [],
      "source": [
        "! eval stringtie -L -o $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/stringtie/${ACC}.gtf -G $ANNOTATION_FILE_PATH $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.sorted.bam "
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "xiPsVkfrUw6S"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{StringTie: transcript assembly - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "or7JeoLlUw6U"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "EWrA0eBPUw6V"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/stringtie $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Y7ib8gNMUw6Y"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "MglPWDSTUw6b"
      },
      "outputs": [],
      "source": [
        "! zip -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/stringtie.zip $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/stringtie/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "EvsEJOAdUw6c"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/stringtie.zip\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "TAN1_OR6TfkL"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{GffCompare: transcript assembly statistics - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "wjUMZNQ0TwR9"
      },
      "source": [
        "GffCompare is a program which can evaluate the specificity and novelty of transcripts within a sample-specific transcriptome to a reference transcriptome (documentation: http://ccb.jhu.edu/software/stringtie/gffcompare.shtml)."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "G3BM5t4ZzVHD"
      },
      "outputs": [],
      "source": [
        "! eval gffcompare -o $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/gffcompare/$ACC -r $ANNOTATION_FILE_PATH -R -Q $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/stringtie/${ACC}.gtf"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "W8SCLFLZUyVs"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{GffCompare: transcript assembly statistics - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "TEKaFxwJUyVs"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "zsj9Lt__UyVt"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/gffcompare $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "kC2Gvg3nUyVu"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "U1eeIJFhUyVv"
      },
      "outputs": [],
      "source": [
        "! zip -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/gffcompare.zip $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/gffcompare/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ic6DjrjFUyVv"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/gffcompare.zip\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "y3bt2k_tBGnT"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{FLAME: gene-specific long-read splice variant annotation - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "kXs3BJZqygs7"
      },
      "source": [
        "Full-Length Adjacency Matrix Enumeration (FLAME) is a program which can detect and quantify novel splice junctions on an annotated gene locus (documentation: https://github.com/marabouboy/FLAME). "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "JB86-GcXZHIT"
      },
      "outputs": [],
      "source": [
        "! eval bedtools bamtobed -bed12 -i $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.sorted.bam > $(eval echo $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bed/$ACC.sorted.bed12)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "_Y4DKdo5LhBB"
      },
      "outputs": [],
      "source": [
        "! eval python3 /content/FLAME/FLAME/FLAME.py -I $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bed/$ACC.sorted.bed12 -GTF $ANNOTATION_FILE_PATH -G $REGION_NAME -O $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/flame/$ACC"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "yNrDbLpg4H6_"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{FLAME: gene-specific long-read splice variant annotation - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "gtxRHyEO4H7A"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "cLxi8NXw4H7C"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/flame $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "lM7C8DCy4H7D"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "KdiyIHxkwdFT"
      },
      "outputs": [],
      "source": [
        "! zip -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/flame.zip $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/flame/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "T3GgoMYP4H7F"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/flame.zip\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "7yVbaSBc5cu7"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{featureCounts: assign sequence reads to genomic features - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "-2kbK23S5oi5"
      },
      "source": [
        "featureCounts is a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments (documentation: http://subread.sourceforge.net/). "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "1ycdSYt_5plb"
      },
      "outputs": [],
      "source": [
        "! eval featureCounts -O -L -a $ANNOTATION_FILE_PATH -t exon -g gene_id -o $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/featureCounts/$ACC.txt $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.sorted.bam "
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "a2s7KTWRw3ry"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{featureCounts: assign sequence reads to genomic features - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ZsTqqT1aw3r0"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "StNofMQFw3r1"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/featureCounts/ $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "jqBqz7Ztw3r2"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "CpJsMgUNVogc"
      },
      "outputs": [],
      "source": [
        "! zip -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/featureCounts.zip $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/featureCounts/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "udK69J1FpWIF"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/featureCounts.zip\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "v8jXqioM50fY"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{LIQA: transcript quantification - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "MrRLmJ1Ojbcc"
      },
      "source": [
        "LIQA is a program which quantifies isoform/transcript expression based on long read RNA sequencing data (documentation: https://github.com/WGLab/LIQA)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "2_zvCVli55EX"
      },
      "outputs": [],
      "source": [
        "! eval liqa -task refgene -ref $ANNOTATION_FILE_PATH -format gtf -out $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/$ACC.refgene"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "Hy-E4YBT7iCr"
      },
      "outputs": [],
      "source": [
        "! eval liqa -task quantify -refgene $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/prebuilt_indices/$ACC.refgene -bam $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.sorted.bam -out $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/liqa/${ACC}_quantification.txt -max_distance 10 -f_weight 1"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "fQy3NibXkZww"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{LIQA: transcript quantification - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "zfLiaJmBkZwx"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "lNQuGyYNkZwy"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/liqa/ $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ZJ50Bs_RkZwz"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "4c9Rnp_HkZwz"
      },
      "outputs": [],
      "source": [
        "! zip -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/liqa.zip $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/liqa/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "TPLA1-_6kZw0"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/liqa.zip\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "VXojzd-9mjPc"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{FusionSeeker: detect gene fusions - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "kAb1EVhSpyhS"
      },
      "source": [
        "FussionCaller is a gene fusion caller for long-read single-molecular sequencing data (documentation: https://github.com/Maggi-Chen/FusionSeeker). "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "_x9eJ_oDmmU8"
      },
      "outputs": [],
      "source": [
        "! eval /content/FusionSeeker/fusionseeker --bam $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.sorted.bam --outpath $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fusionseeker/ --ref $INDEX_FILE_PATH --gtf $ANNOTATION_FILE_PATH "
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "veJUugPx8-Q_"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{FusionSeeker: detect gene fusions - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "A9IgEX-88-RE"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "nx5uVzJX8-RF"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fusionseeker $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "6JwKYuga8-RG"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "aO9VI51c8-RI"
      },
      "outputs": [],
      "source": [
        "! zip -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fusionseeker.zip $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fusionseeker/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ge2aCdde8-RJ"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/fusionseeker.zip\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "S9r4MCB0lvAf"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{svist4get: visualize genomic tracks from sequencing experiments - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "3T2Y3dcAnaWu"
      },
      "source": [
        "svist4get allows you to view read coverage at a defined region on a chromosome (documentation: https://bitbucket.org/artegorov/svist4get/src/master/)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ehHeatJQCZ42"
      },
      "outputs": [],
      "source": [
        "! eval bedtools genomecov -split -ibam $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.sorted.bam -bg > $(eval echo $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bed/$ACC.sorted.bedgraph)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "OpQMW3gI15ZI"
      },
      "outputs": [],
      "source": [
        "! eval svist4get -bg $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bed/$ACC.sorted.bedgraph -gtf $ANNOTATION_FILE_PATH -fa $INDEX_FILE_PATH -bl Long-Read Coverage -w $CHROMOSOME $CHROMOSOME_START $CHROMOSOME_FINISH -it \"$REGION_NAME\" -o $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/svist4get/$ACC"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "emZMFcIZ4Z7q"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{svist4get: visualize genomic tracks from sequencing experiments - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "rB3h07vK4Z7s"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "HY784C9N4Z7t"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/svist4get/ $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "w6hQ-NhH4Z7u"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "c9bDP-P1vvA4"
      },
      "outputs": [],
      "source": [
        "! zip -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/svist4get.zip $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/svist4get/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "XyJTQFQZ4Z7w"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/svist4get.zip\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "MjZ_tYz4pEHX"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{Pistis: quality control plotting for long reads - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "RFhhJITCphA_"
      },
      "source": [
        "Pistis generates long-read specific quality control graphs, including a plot demonstrating read alignment percentage to the reference genome (documentation: https://github.com/mbhall88/pistis)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "B5Zv-aSzVPwK"
      },
      "source": [
        "Please note that the report generates assuming alignment of more than 50,000 reads. If this is not the case, please add the flag `--downsample INTEGER` replacing `INTEGER` with a number less than the number of aligned reads. Additionally, please ignore deprecation warnings. "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ik-boaBxeNjP"
      },
      "outputs": [],
      "source": [
        "! eval pistis --downsample 4000 -f $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/fastq/$ACC.fastq -b $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.sorted.bam  -o $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/pistis/$ACC.pdf"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ZzePzpXU48T0"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{Pistis: quality control plotting for long reads - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Ev9sTiLI48T2"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "rUoqVlq548T3"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/pistis/ $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "_XM7DHSH48T4"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "uPjj7MrHa23h"
      },
      "outputs": [],
      "source": [
        "! zip -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/pistis.zip $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/pistis/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ToqqgNwD48T7"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/pistis.zip\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "POLtVVCEKndf"
      },
      "source": [
        "##$\\color{#2977d6}{\\text{MakeHub: generate UCSC assembly hubs - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ZcW7zXOoKrCy"
      },
      "source": [
        "MakeHub is a command line tool for the fully automatic generation of of track data hubs for visualizing genomes with the UCSC genome browser (documentation: https://github.com/Gaius-Augustus/MakeHub)."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "fMN2TYdniufR"
      },
      "outputs": [],
      "source": [
        "! chmod 755 $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/makehub/make_hub.py"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "pVA2mrrjZ2yM"
      },
      "outputs": [],
      "source": [
        "! eval $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/makehub/make_hub.py -l $HUB_KEYWORD -L $HUB_NAME -g $INDEX_FILE_PATH -e \\\n",
        "  $HUB_EMAIL -a $ANNOTATION_FILE_PATH -b $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/bam/$ACC.sorted.bam -o $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/makehub/"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "E2nQAifZ6Fn9"
      },
      "source": [
        "##$\\color{#4f7bb0}{\\text{MakeHub: generate UCSC assembly hubs - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "NTlyCHAj6Fn_"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "OyvrqB4n6FoA"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/makehub $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "AB1LYUCh6FoA"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "u_2BDvY0bz8Y"
      },
      "outputs": [],
      "source": [
        "! zip -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/makehub.zip $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/makehub/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "-vJjpEWh6FoD"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/makehub.zip\"]))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "m5pU9i4DvGxQ"
      },
      "source": [
        "##$\\color{#d42bb4}{\\text{MultiQC: aggregate bioinformatics analysis - usage}}$"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "sPB5udNzvVdJ"
      },
      "source": [
        "MultiQC is a program which allows you to combine reports for as many samples as you wish ([documentation](https://multiqc.info/docs/))"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "SEBsMVQ5OG4U"
      },
      "outputs": [],
      "source": [
        "! eval multiqc $PIPELINE_FILE_PATH/long-read-sequencing-pipeline -o $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/multiqc/$ACC.pdf"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "n-WhLFAz5e0s"
      },
      "source": [
        "##$\\color{#a7588f}{\\text{MultiQC: aggregate bioinformatics analysis - export}}$\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "n98P06aH5e0t"
      },
      "source": [
        "To Store Resulting Files in your Google Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "28HahdKB5e0u"
      },
      "outputs": [],
      "source": [
        "! cp -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/multiqc/ $STORAGE_FILE_PATH"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "FmRDMa3Q5e0v"
      },
      "source": [
        "To Store Resulting Files in your Local Hard Drive: "
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "mj5NMZTucrsV"
      },
      "outputs": [],
      "source": [
        "! zip -r $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/multiqc.zip $PIPELINE_FILE_PATH/long-read-sequencing-pipeline/multiqc/"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "5o0K3bsz5e0x"
      },
      "outputs": [],
      "source": [
        "from google.colab import files\n",
        "import os\n",
        "\n",
        "files.download(\"\".join([os.environ[\"PIPELINE_FILE_PATH\"],\"/long-read-sequencing-pipeline/multiqc.zip\"]))"
      ]
    }
  ],
  "metadata": {
    "colab": {
      "collapsed_sections": [
        "AUKHTlobUcf_",
        "RrTcAlHtbWfg",
        "z1lysGn4hO-i",
        "F0hFNwmcv5qr",
        "k_oe5__lB6Lz",
        "gyh52FxVTSQt",
        "dxspwFM3_1qN",
        "Y9qrP4Ip3xwz",
        "3U_BpHSJA9Xe",
        "yhR96h7O5CHN",
        "vZPSGeXlh7kh",
        "oOS4NvQ8o5Q7",
        "EFHE0ybf9rRI",
        "CId-MKlu9uMZ",
        "npZwllsupfEJ",
        "5CwywN4tc74s",
        "EQn9Ikb3YkFC",
        "kpfzCCTKuqMt",
        "oBdBA_CDdE0z",
        "_MislmkXZcz-",
        "SQb5HTiwtfMn",
        "NOrgEp-fbtBt",
        "7uHwZ4Zj1vgC",
        "D6iKV4YDiJQk",
        "EJ0KI6ZxJInS",
        "oBPQyTcKOPDF",
        "f8EfwQZze29B",
        "J_OH_OItuBjO",
        "sjns1XbAkILI",
        "swcyphLAvE52",
        "zqQcBdxa4X7q",
        "iUwbIIRkwWrL",
        "BKjT28HjsBkW",
        "xiPsVkfrUw6S",
        "TAN1_OR6TfkL",
        "W8SCLFLZUyVs",
        "y3bt2k_tBGnT",
        "yNrDbLpg4H6_",
        "7yVbaSBc5cu7",
        "a2s7KTWRw3ry",
        "v8jXqioM50fY",
        "fQy3NibXkZww",
        "VXojzd-9mjPc",
        "veJUugPx8-Q_",
        "S9r4MCB0lvAf",
        "emZMFcIZ4Z7q",
        "MjZ_tYz4pEHX",
        "ZzePzpXU48T0",
        "POLtVVCEKndf",
        "E2nQAifZ6Fn9",
        "m5pU9i4DvGxQ",
        "n-WhLFAz5e0s"
      ],
      "machine_shape": "hm",
      "provenance": []
    },
    "gpuClass": "standard",
    "kernelspec": {
      "display_name": "Python 3",
      "name": "python3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "nbformat": 4,
  "nbformat_minor": 0
}