Splitting Fused genes

[shanebrubaker]

Hi, I am using software such as cufflinks to create transcriptome assemblies. However, I have a very compact genome, and so end up with a lot of long, fused transcripts, often containing 2 or more genes.

I was wondering if there was any way to control for this or to split the genes apart again. I see a lot of software that is designed to try and find gene fusion events, but nothing to split them back apart.

[Wallysb01]

Do you happen to have strand specific RNA-seq data? Otherwise you might not be able to do much with cufflinks assemblies regarding this problem. Its possible something like Trinity then PASA would work better in your situation for both strand specific and non-stranded libraries.