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Old 03-26-2013, 10:59 AM   #3
Location: Bethesda, MD

Join Date: Oct 2010
Posts: 47

I mean a file with defined transcripts and their corresponding exon coordinates to use with the counting software.

The tophat output gives my reads mapped to the entire genome (mm10 in this case) then for the next step, I use a transcriptome file that has defined transcripts with exon coordinates. I am interested in obtaining read counts that align to each transcript or to each transcripts exons in the file.
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