How to improve genome annotation by RNA-seq?

[xmubingo]

Hi everyone!

Recently, I got a RNA-seq data of species X. As far as i know, original annotation of species X was generated by Ensembl pipeline. After i ran "tophat->cufflinks->cuffcompare", i found many novel features from assembled transcripts. For example, novel transcripts and novel 5'/3' UTR were found.

My question is, how can i improve the original annotation file(GFF3) by drawing knowledge from RNA-seq data ? Is there any software can do this?

Thanks a lot!!

[Wallysb01]

PASA is what you’re looking for.

[xmubingo]

PASA is what you’re looking for.

Thanks! I am reading the manual of PASA.