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README.Rmd
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---
title: "Insights into rRNA processing and modifications in Archaea using Nanopore-based RNA sequencing"
author: |
| <a href="https://orcid.org/0000-0001-7444-2408">Felix Grünberger<sup>1</sup></a>, Michael Jüttner, Robert Knüppel, <a href="https://orcid.org/0000-0002-0522-843X">Sébastien Ferreira-Cerca<sup>2</sup></a>, and <a href="https://orcid.org/0000-0002-0570-2517">Dina Grohmann<sup>1</sup></a>
|
<sup>1</sup> Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab & Biochemistry Centre Regensburg, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
<sup>2</sup> Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
output:
github_document:
toc: false
toc_depth: 4
highlight: github
bibliography: "/Users/felix/Documents/library_nanopore.bib"
link-citations: true
always_allow_html: true
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
*********
## About this repository
This is the repository for the manuscript "Insights into rRNA processing and modifications in Archaea using Nanopore-based RNA sequencing".
The repository is currently actively developed.
[](https://gist.github.com/cheerfulstoic/d107229326a01ff0f333a1d3476e068d)
<!--## Full documentation here
https://felixgrunberger.github.io/rRNA_maturation/
-->
## Preprint
This work is based on our previous preprint:
[Exploring prokaryotic transcription, operon structures, rRNA maturation and modifications using Nanopore-based native RNA sequencing.]("https://www.biorxiv.org/content/10.1101/2019.12.18.880849v2.full")
## What can you find here
A description of the workflow using publicly available tools used to basecall, demultiplex, trim and map (*direct cDNA*) data and data preparation for modified base detection (*using direct RNA*) can be found in the [pipeline](pipeline) section.
Downstream analysis, including
- quality control
- detection of rRNA processing sites and classification of rRNA intermediates
- Circular RNA detection
- Modified base detection
are based on custom Rscripts that are also described in the [pipeline](pipeline) section.
## Data availability
Raw direct RNA data (gzipped raw FAST5 files) have been uploaded to the Sequence Read Archive (SRA) and are available under project accession number [PRJNA632538](https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA632538) (WT run: SRR11991303, ∆KsgA run: SRR11991308).
Direct cDNA data are available at the European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) under project accession number PRJEB57168.
ERP142133
ERR10466882
*********
## License
This project is under the general MIT License - see the [LICENSE](LICENSE) file for details