RNAseq splicing tools

Question

[saroushka]

Hi,

I am using the Cufflinks suite to perform de novo transcript assembly. At the same time, I am interested on the splicing events, for that I am using rMATS. I was wondering if it would be possible to integrate the new gtf obtained by cuffmerge to the rMATS program in order to integrate the new exons/transcripts in the counting of the events by rMATS? Or if there is somehow a way to link the output of Cufflinks-Cuffdiff and rMATS?

Thanks a lot.

Answer 1

[noahhelton98]

Yes just input the path to the merged gtf file: rmats.py --gtf /path/to/merged.gtf

They have answered this in their FAQs as well http://rnaseq-mats.sourceforge.net/rmats3.2.4/faq.html

[saroushka]

Thanks a lot for your answer!