On Mon, Nov 26, 2012 at 6:47 PM, Zhiqiang Shu <[email protected]> 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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
