On Mon, Nov 26, 2012 at 6:47 PM, Zhiqiang Shu <zshu@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? Peter