Finding SNV showing allele specific bias
0
0
Entering edit mode
2.9 years ago
ishmahe16 • 0

I have a fastq.gz file. I want to know the SNV's in this file showing an allele specific bias ( Bias as SNV allele frequency >0.7) .How can I do that?

rna-seq gene • 647 views
ADD COMMENT
3
Entering edit mode

You're going to have better luck getting useful answers if you a) show evidence that you've tried to research this problem yourself b) tell us what you've tried, and c) provide more details

ADD REPLY
0
Entering edit mode

So i had 6 files 3 control and 3 primed files and had to find the most differentially expressed gene. Usong Galaxy I did FastQc then trimmed the seauences. Once that was done I did RNA STAR to aloign them followed by htseq Count . Once I had the bam files I did deseq2 and got the genes that I am looking for.

For the SNV thing I tried converting the bam file to bcf using samtools and then to vcf file . Once I had my vcf file I had done grep -c AF1 but I am stuck at that point.

ADD REPLY

Login before adding your answer.

Traffic: 2182 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6