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Old 08-20-2016, 09:21 AM   #45
Senior Member
Location: NC State, Raleigh, NC

Join Date: Mar 2013
Posts: 107


Thanks again for your quick replies. I just wanted to mention that I really appreciate your last response. While you may not be interested, I wanted to describe for others at least how I was not using the HtSeq-count tool/workflow properly. Instead of using the genome fasta file, I was using a multi-fasta file (cds only). Once I used the genome fasta file, almost everything worked properly. The one issue I ran into was that HtSeq count did not recognize the values in the first column of the GFF3 file. The reason was because the value in the first column was different from the sam file headers. The way I solved this was by changing the genome fasta file header to value in the first column of the GFF3 file before mapping.

Thank you and God bless,
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