This is a test version of Biostars. For the public version, visit https://www.biostars.org.
RNAseq splicing tools

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.

rna-seq alternative splicing studies
• 1,160 views • link
updated by noahhelton98 • noahhelton98 • written by saroushka • saroushka

1 answer

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

• 0 views • link
written by noahhelton98 • noahhelton98

Log in to answer this question.

More posts like this