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Old 02-20-2017, 11:36 PM   #2
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Join Date: Oct 2011
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I don't know if it's a good idea to do it this way, since you'll get a higher amount of overlapping features. I hope you have a stranded library.

Nevertheless, in order to get what you described you'll need a GTF which has also "transcript" in the third field ( head -n 1000 my.gtf | cut -f 3 | sort -u ; should also report transcript). ENSEMBL's gtf has it for instance.
With such a gtf, you can use this feature type instead of exons for counting:

htseq-count -t transcript my_alignment.sam my.gtf


Last edited by Michael.Ante; 02-20-2017 at 11:41 PM.
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