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?
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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.
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