Novel Exon Discovery in RNA Seq

Question

[andrew.j.skelton73]

Hi

I've used the tuxedo pipeline and I'd like an alternative for detecting novel exons in aligned reads. Does anyone know of any tools that will do something like that?

Thanks

Answer 1

[Pascal]

Similar to cufflinks you could try Scripture, but the last time I tried it I got an extremely high number of isoforms for some genes.

Another program is SpliceGrapher, which I never tried before.

[andrew.j.skelton73]

That's great, Thanks!