View Single Post
Old 06-07-2013, 03:22 PM   #14
muthu545
Member
 
Location: san antonio

Join Date: Jul 2011
Posts: 32
Default

Hi,

I'm am novice to using DEXSeq.
@zimmernv and @Alejandro
How could you get the flattened GTF file with 'real' exons instead of the exonic parts?

Thanks
--
Muthu

Quote:
Originally Posted by areyes

I guess the exon bining is an attempt to test for all possible exon usage regulation according by testing all unique non-overlapping exonic parts from any transcript, but at the end its an optional step. You could input in DEXSeq with "real" exons. My guess is that it won't make a huge difference, but let me know if I am wrong!

Quote:
Originally Posted by zimmernv

I tried it again with "real" exons, and I got 1 differentially-expressed exon rather than 0. So, as you implied, the difference is not substantial (though that 1 hit is very interesting as far as the biology is concerned).
muthu545 is offline   Reply With Quote