counting the reads mapped only to the coding sequence
I have aligned the RNAseq data to the transcriptome and have .bam files. now I want to count the reads that map to the coding sequence not the whole transcriptome. I usually use HTseq count to do so. do you guys know how to do that?
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h.mon
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alirezamomeni707 •
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alirezamomeni707 •
2 answers
Did you look at this answer?
Why don't you tell exactly what you did - commands included?
Usually, when reads are aligned to a transcriptome, one uses RSEM or eXpress (or some other expectation-maximization algorithm) to perform quantification of transcript expression.
Now, in case you aligned to the genome and have a gene annotation, you can use HTSeq or (better) featureCounts to perform quantification of gene expression.
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So what's the problem then? Seems you already know the solution.