-m option of HTSeq in featureCounts

Question

[Apex92]

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.

[Asaf]

Are you sure you want HTSeq-count? There are better tools for evaluating transcript levels nowadays, if this is what you are indeed doing.

[Apex92]

I want to use featureCounts but not sure how to specify the mapping option as I did in HTSeq count (-m intersection-nonempty)

Answer 1

[Istvan Albert]

featureCounts does not implement all the features of htseq-counts. Conceptually the tool works differently and uses different internal representations.

I don't think that the intersection-nonempty mode is implemented.

[Apex92]

Thank you for the comment. With that being said, I go with the default version of alignment mode in featureCounts, is it ok?

[Istvan Albert]

you should think about why you want that to be set and what it actually means in the larger context.

why would you want that parameter to be set? is it because you want one feature to be fully covered, or completely included? etc perhaps other parameters of featureCounts do an even better job achieving that goal.

in my opinion the example in the htseq count documentation does not fully explain and define what intersection-nonempty does