TIPseqHunter example

TIPseqHunter Example

A zip archive containing example files can be downloaded from the following link tipseqhunter_example.tar.gz

This example file makes use of simulated TIPseq data.

tipseqhunter_example
├── bam
│   ├── tipseq.chr22.example.bam
│   └── tipseq.chr22.example.bam.bai
├── insertion_sites.repred
└── reference
    ├── Homo_sapiens_L1.L1HS.fa
    ├── Homo_sapiens_L1.L1HS.fa.fai
    └── hg19
        └── chr22.fa

Filename	Description
/bam/tipseq.chr22.example.bam	bam file containing reads aligned to the hg19 reference genome
/bam/tipseq.chr22.example.bam.bai	BAM index file
insertion_sites.repred	Defines the regions flanking the insertions
/reference/Homo_sapiens_L1.L1HS.fa	reference sequence for the mobile element
/reference/Homo_sapiens_L1.L1HS.fa.fai	FASTA index file
/reference/hg19/	Folder containing the reference genome chromosomes
/reference/hg19/chr22.fa	This example only contains insertions in chromosome 22

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Processing the example with TranspoScope

To run TranspoScope using the example files, first install TranspoScope (instructions).

Next, download the example archive (tipseqhunter_example.tar.gz) and navigate to the directory in which the file was downloaded.

Then:

1. Extract the files

tar -zxvf tipseqhunter_example.tar.gz

2. Navigate to the extracted directory

cd tipseqhunter_example

3. Run TranspoScope align

transposcope align tipseqhunter insertion_sites.repred bam/tipseq.chr22.example.bam reference/Homo_sapiens_L1.L1HS.fa reference/hg19/ tipseqhunter_example

4. Two folders will be created, 'output' and 'web'. To view the coverage using the viewer run:

transposcope view web

5. To stop the viewer press ctrl+c when the terminal window is selected