I've done RNA-seq of a number of samples, I've aligned them with Tophat2 and I've done some interesting analyses with DESeq2, but now I would like to look at the actual sequences. As far as I can understand, that should be possible, using the accepted_hits.bam files I have after the alignment.
What I want to do is basically look at the sequences for each bam-file I have, for an arbitrary gene, and see how that gene's sequence differs in my samples from a reference and its sequence for that gene (I'm using hg19 from iGenomes).
Exactly does one go about doing this? I've looked around, and using SAMTOOLS FAIDX seems to be a part of it, though I don't understand how I get my actual bam-files into that workflow...
What I want to do is basically look at the sequences for each bam-file I have, for an arbitrary gene, and see how that gene's sequence differs in my samples from a reference and its sequence for that gene (I'm using hg19 from iGenomes).
Exactly does one go about doing this? I've looked around, and using SAMTOOLS FAIDX seems to be a part of it, though I don't understand how I get my actual bam-files into that workflow...
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