Question: frequency of each nucleotide at each position in sequence
0
gravatar for Sara
19 months ago by
Sara30
Sara30 wrote:

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?

rna-seq • 645 views
ADD COMMENTlink modified 19 months ago by george.ry1.1k • written 19 months ago by Sara30

I think you are referring to calling variant ?!
something like:

https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq

ADD REPLYlink modified 19 months ago • written 19 months ago by Medhat8.2k
0
gravatar for george.ry
19 months ago by
george.ry1.1k
United Kingdom
george.ry1.1k wrote:

If you're not looking to call the variants as Medhat says, then bam-readcount will do this.

ADD COMMENTlink modified 19 months ago • written 19 months ago by george.ry1.1k
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