-m option of HTSeq in featureCounts
1
0
Entering edit mode
9 months ago
Apex92 ▴ 50

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.

sequencing gene rna-seq next-gen • 258 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
9 months ago

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1825 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6