Hi,
I ran HTSeq on a *.sam file using RefSeq genes GTF file. I got counts for each transcript and would like to understand how exactly these counts were generated. Does HTSeq count a read whenever it overlaps with an exon and then takes a sum/average of all these exons across a transcript? Or, is there some other complicated procedure to merge the counts of all the exons in a transcript?
Thank you very much for your response.
Nirmala
I ran HTSeq on a *.sam file using RefSeq genes GTF file. I got counts for each transcript and would like to understand how exactly these counts were generated. Does HTSeq count a read whenever it overlaps with an exon and then takes a sum/average of all these exons across a transcript? Or, is there some other complicated procedure to merge the counts of all the exons in a transcript?
Thank you very much for your response.
Nirmala
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