htseq-count: -s reverse vs -s stranded

Question

[simonjean434]

Hello,

I have RNASeq paired-end data (library type dUTP). I would like to use htseq-count to get coverage of genes but I am not sure which option I should use -s reverse or -s stranded.

Thanks
Jean

Answer 1

[Ido Tamir]

It will probably be -s reverse, but simply do both and you will immediately be able to see which one was correct. Other options: look in genome browser, http://rseqc.sourceforge.net/#infer-experiment-py

Answer 2

[Ben]

I found this useful: