Which htseq-count mode to use for handling overlaps during RNA-Seq quantitation
For counting gene expression levels (paired end stranded RNA-Seq data from mouse) using htseq-count, is there a universally accepted mode to use from the following list?
--mode union
--mode intersection-strict
--mode intersection-nonempty
To me, "union" seems like the appropriate choice but the wiki here suggests "intersection-strict" is best.
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lieven.sterck
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skhan •
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skhan •
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In most cases: yes, intersect-strict is the most appropriate one.
take a look here to see what the difference in behaviour of htseq is for the different modes. Depending on what you want to know/count you can switch to any of the other modes
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