Hi,
I notice in my sequencing result that, the reads are not strand specific. There are lots of read matching the opposite strand of mRNA. There is a "--stranded=no" option in HTseq. But I didnot find any similar option in cuffdiff. May I ask whether there is such option in cuffdiff? And, how cuffdiff deals with reads matching opposite strand or genes with no strand information (e.g. "." for strand information)?
Cheers,
Jun
I notice in my sequencing result that, the reads are not strand specific. There are lots of read matching the opposite strand of mRNA. There is a "--stranded=no" option in HTseq. But I didnot find any similar option in cuffdiff. May I ask whether there is such option in cuffdiff? And, how cuffdiff deals with reads matching opposite strand or genes with no strand information (e.g. "." for strand information)?
Cheers,
Jun
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