How to retrieve RNA sequences

Question

[sdf.ambreen]

I have cuff-merge results, its provide me coordinates of genome. I retrieve the genomics sequences of these transcripts. I have a confusion. This is Gene (DNA)sequences of this transcripts, how i can get the RNA sequences data.?

Answer 1

[Devon Ryan]

You can use gtf_to_fasta from tophat. It'll give you the spliced transcripts.