frequency of each nucleotide at each position in sequence
I have aligned RNAseq data and now I have bam files for control and treated conditions. I am trying to get the frequency of each nucleotide at each position in a sequence of 95 nt. to get the mutation rate at each position. except for the igv, is there any way to do that?
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davidhugh767 •
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Sara
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Sara
1 answer
If you're not looking to call the variants as Medhat says, then bam-readcount will do this.
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I think you are referring to calling variant ?!
something like:
https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq