htseq-count: -s reverse vs -s stranded
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
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Ram
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simonjean434 •
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simonjean434 •
2 answers
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
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