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Old 04-07-2014, 04:12 AM   #4
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

htseq-count won't double count reads mapping to multiple exons, since it's designed with gene-level analyses in mind. The scripts that come with DEXSeq are different in this regard, since there it makes sense to double count in these instances (the DESeq/DEXSeq authors put enough thought into things that you won't normally shoot yourself in the foot doing this sort of thing). If you used the default "-t exon -i gene_id" then what you're telling the script to do is to look at reads mapping within exons and then count them according to how they overlap genes denoted by their gene_id. This is normally the appropriate way to go about things.
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