Hi,

I'm trying to run TopHat as a first step of a de-novo transcript assembly project that I'm doing, and I saw that on 2010 it was said on a different forum that there's a class of genes for which Tophat is unable to find the spliced junctions- the genes that generate duplicates through retrotransposons.

In my case, I am interested in finding transcripts that start from a re-activated transposable element in the genome, so I would like to know if this default option in Tophat still exists, and if so, how can I overcome it?

When I run Tophat on my data I only receive 1 region with a splice junction so I figured that it has something to do with this. If this happens due to a different reason, it would be nice if you could enlighten me!

Thanks,
Oran