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