Hi. This is my first time using featureCounts
and I need your help (🚨). I have single-end reads and used HTSeq-count
several times with the -m (mode
) option specified to --intersection-nonempty
https://htseq.readthedocs.io/en/release_0.11.1/count.html. However, I am now trying to run featureCounts and not 100 percent sure that which option of in the featureCounts
is equal to -m intersection-nonempty
in HTSeq-count
.
Any help will be appreciated.
Thanks.
Are you sure you want HTSeq-count? There are better tools for evaluating transcript levels nowadays, if this is what you are indeed doing.
I want to use featureCounts but not sure how to specify the mapping option as I did in HTSeq count (
-m intersection-nonempty
)