On Mon, Nov 26, 2012 at 6:47 PM, Zhiqiang Shu <z...@bio.fsu.edu> wrote:
> Hi, Galaxy users!
> I have a question on how to find out sense and antisense sequence. I've got
> RNA seq data in the fastq format. The sequences inside are partially
> complementary to each other (complementary is 10nt, while entire is about
> 30nt). How can I separate these sequences into two groups: sense and
> antisense

Depending on how your sequences were prepared, you might be able to
look for a poly-A tail as a clue to orientation. Another approach is to
compare the (assembled) transcripts to known genes and if you only
get matches on one strand that is probably the correct orientation.

> (one thing I know is for the sense sequence the 10th nucleotide is
> always "A")?

Why is that? Is this related to your library preparation?

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