Question Of Calculating Counts For Strand-Specific

Question

[camelbbs]

Hi all,

Can anybody address these 3 questions in calculating counts for strand-specific by HTseq-count.

1. How the HTseq-count calculate counts for strand-specific RNAseq. I want to ask the principle of it.

2. After I checked the Refseq database, I found about 280 genes have two copies in different strand (and different location). Although most of the genes don't have this problem. While HTseq-count calculate the counts, how does it deal with this issue.

3. Can I compare the gene expression (rpkm or counts) from the strand-specific library and from unstranded library?

Thanks a lot!!

Cam

[Eric Normandeau]

Hi Camelbbs. I'm adding this comment to all your questions: Please take some time, before you ask a question, to think more about your problems and most likely sources of answers (manuals, FAQs, Google!, etc.). When you ask a question, include some context, tell us why you ask that question, what result you need, etc. Most of your questions are vague, impossible to answer or you changed them following an answer because it became evident that it was not clear. Cheers.

Answer 1

[Mikael Huss]

Yes, it does. See: http://www-huber.embl.de/users/anders/HTSeq/doc/count.html

By default, it assumes strand-specific RNA-seq. To turn this off (as I usually do since I mostly analyze unstranded), add '-s no' to the command line.

[camelbbs]

Thanks but I think that's not I am asking. I modified my question.