rMATS User Group

rMATS can process each BAM file on a separate thread so you could use as many threads as you have BAM

Yes, you can run the prep step on each sample separately, then run a single post step with all the

The parameter details you posted are mostly correct For the prep step, --bi BINDEX is required if

https://github.com/Xinglab/rmats-turbo/issues/531 > When the statistical test is run, the final

Hi Eric, Thank you for the clarification. I had initially understood that to detect intron retention,

Hi Xiao, rMATS only considers two isoforms for each event. The inclusion level is a ratio of reads

anyone interested?

Hey everyone! This $159 offer is only valid until December 25. After that, the price goes up to $259.

Here's the post saying pvalue=0 can be interpreted as less than 2.2e-16: https://groups.google.

Hi Eric apologies for the delayed reply, I wanted to say thanks for your response. I did process each

Coordinates are reported in genomic order regardless of strand. The retained intron is upstreamEE to

--task both runs prep and post. Usually post includes stat, but --statoff causes the post step to

Thanks, I'll take a look. On Mon, Sep 22, 2025 at 9:00 PM Thomas Danhorn <tdan...@gmail.com

Here's the post you mentioned: https://github.com/Xinglab/rmats-turbo/issues/17 That post

It could be that your read length is not exactly 100. You can look at some individual alignments to

The read support for a 3 exon sequence actually is not from a read with 2 junctions, but from a

See this post about interpreting IncLevelDifference: https://github.com/Xinglab/rmats-turbo/issues/

The start coordinates are always 0-based while the end coordinates are always 1-based: https://github

Tumor-.txt changes to s2.txt Normal.txt changes to s1.txt and follow the instructions of https://

Now it works, the same code didn't work yesterday, but it works today😊 On Thu, 24 Apr 2025 at 11:

To get a primer specific for a particular splice junction, make sure it is right on top of it, so

Good morning all, I am very new to Rmats but i am curious whether there are tools available to

One source of the difference could be that rMATS is looking for specific event types (SE, A5SS, A3SS,

This post has some details about how events are detected and also filtered: https://github.com/

That syntax error could happen if you attempt to install the python 3 version of the rmats2sashimplot

Ok thanks to your links to related conversations with similar problems, i realized that I forgot my

Answered at https://github.com/Xinglab/rmats-turbo/issues/468 On Tuesday, January 28, 2025 at 11:01:

Hi, Yeah, you are right. The read length is bit short for the splicing analysis. But i have decent

Thanks so much, Eric, for the detailed response and the links! The explanation of how rmats2sashimi

This website does seem to be down http://rmaps.cecsresearch.org/ You could try contacting the authors

The diagram in the README shows which reads count toward the inclusion or skipping isoform of each