Question

htseq-count: -s reverse vs -s stranded

2

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10.5 years ago

simonjean434 ▴ 70

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

RNA-Seq • 9.4k views

ADD COMMENT • link updated 3.3 years ago by Ram 45k • written 10.5 years ago by simonjean434 ▴ 70

Ram · Answer 1 · 2015-04-22

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10.5 years ago

Ido Tamir 5.2k

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

ADD COMMENT • link updated 3.3 years ago by Ram 45k • written 10.5 years ago by Ido Tamir 5.2k

score 1 · Answer 2 · 2016-06-27

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9.3 years ago

Ben • 0

I found this useful:

ADD COMMENT • link 9.3 years ago by Ben • 0