Question: Which htseq-count mode to use for handling overlaps during RNA-Seq quantitation
gravatar for skhan
2.4 years ago by
skhan10 wrote:

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.

rna-seq htseq-count • 1.6k views
ADD COMMENTlink modified 2.4 years ago by lieven.sterck8.6k • written 2.4 years ago by skhan10
gravatar for lieven.sterck
2.4 years ago by
VIB, Ghent, Belgium
lieven.sterck8.6k wrote:

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

ADD COMMENTlink written 2.4 years ago by lieven.sterck8.6k
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