When I used rMATS to study differential alternative splicing, I found a problem. I got the bam file through tophat, then I was running the rMATS and I need a gtf file. Should I use the reference genome annotation file or the annotation file assembled by cufflinks and cuffmerge? I'm just a beginner in bioinformatics,please help me,thanks!
I thought there was something unique about their reference format, but they also provided the reference files.
May be an issue if you have a non-model species, but I think the answer is "possibly not?"
At first, I thought you might have had to go back to rMATS 3 to find the reference .gtf files (in the gtf subfolder)?
https://sourceforge.net/projects/rnaseq-mats/files/MATS/rMATS.3.2.5.tgz/download
However, I think those are also available separately (but there was a link to the wrong download location, somewhere else):
https://sourceforge.net/projects/rnaseq-mats/files/MATS/gtf.tgz/download
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