Originally posted by ThePresident
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BTW, the ability of htseq-count to discriminate between unique and multimappers is aligner dependent. You mention using bowtie (I'll take that to mean tophat, unless your organism doesn't do splicing), so it should then have the NH auxiliary tag properly set. When in doubt, use the "-o" option of htseq-count to follow how reads are being treated. Then you can determine if there's anything really amiss.
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