yhoogstrate / fibronectin-splice-variant-detector

fibronectin-splice-variant-detector

fibronectin-splice-var-determiner

This application investigates/counts 2 splice isoforms in the gene FN1 in RNA-seq data: 7B89 and 11A12.

Using RNA-seq, variants can be determined based on reads that:

• (1) fall exactly over the splice junction (use -s / --spliced-only)
• (2) are 'spanning' the splice junction and are thus mapped perfectly within exons 1 and 8

The only thing that you need are properly aligned RNA-seq BAM files and this tool.

This package is derived from the EGFRvIII determiner application:

10.1093/neuonc/noab231

How to install and test

As provided in ./quick_test.sh:

#!/bin/bash

if [ ! -d ".venv" ] 
then
    virtualenv -p python3 .venv
fi

if [ ! -r "tmp/test_001.bam.bai" ] || [ ! -r "tmp/test_001.bam" ] 
then
    samtools view -bS tests/data/test_001.sam > tmp/test_001.bam
    samtools index tmp/test_001.bam
fi

source .venv/bin/activate
pip install -e .


mkdir -p tmp/

python bin/fibronectin-splice-var-determiner -r hg38 -s -n tmp/test_001.bam > tmp/test_001_sj_01.txt
python bin/fibronectin-splice-var-determiner -r hg38 -s    tmp/test_001.bam > tmp/test_001_sj_02.txt

python bin/fibronectin-splice-var-determiner -r hg38 -n    tmp/test_001.bam > tmp/test_001_cov_01.txt
python bin/fibronectin-splice-var-determiner -r hg38       tmp/test_001.bam > tmp/test_001_cov_02.txt

What is does

We designed a small python tool for estimnating the read counts and/or extracting the actual read names that allows to further analysed the sequencing data.

$ fibronectin-splice-var-determiner -r hg38 -s tmp/test_001.bam

Will result in a text file like this:

sample	7B89: wt reads [24 -> 26]	7B89: sv reads [24 -> 25]	7B89: sv reads [25 -> 26]	7B89: sv reads [24 -> 25 -> 26]	7B89: discrepant reads	11A12: wt reads [31 -> 33]	11A12: sv reads [31 -> 32]	11A12: sv reads [31 -> 32]	11A12: sv reads [31 -> 32 -> 33]	11A12: discrepant reads
tmp/test_001.bam	1	1	1	1	1	1	1	1	0	0

Genomic reference

The genomic reference (hg19/hg38) can be changed using the -r or --reference-build argument. Genomic references starting with '>1' rather than 'chr1' will be automatically resolved.

LICENSE

This is FREE software without liability or warranty, following the GPL-3 software license.