Finding Exon-Intron Junctions without a reference genome
 

Hi,
I'm trying to find intron-exon junctions in assembled transcriptome data without a reference genome. Does anyone know of a tool that can do this?

In general this is an underdetermined problem; most of the information for making the splice lies in the introns. There is a weak signal left behind, but not much.

Your best bet is probably to compare your assembled RNA to the closest relative you can find with this information.

Finding Exon-Intron Junctions without a reference genome
 

Thanks for the advice. I'll try using a relative.

Hi,

You may try Cufflinks or Scripture to let the software figure out the intron/exon junctions for you.

Douglas
www.contigexpress.com