rMATS User Group

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

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

ubuntu (preview) to run test bam file get EventType EventTypeDescription TotalEventsJC

This is very helpful and clears up our confusion. Thank you for your prompt response! On Monday,

Hi Mahek, You can have any number of samples in the two groups. Since you have 5 in group 1 and 13 in

Having different numbers of samples in the two groups should be fine. One possible reason for the 70

rMATS will only detect an event if there is evidence for all exons and splice junctions in the event.

The image in the link is too dark to see clearly. I also wonder why rMATS does not output a variance

No problem at all! It turns out it was a mistake with the readLength setting. Is it possible to

Many thanks for your email. The Python script works. I have one more question. How can the average

Hi, Eric, I see. Thank you for the clarification. Best, Xiao On Mon, Oct 28, 2024 at 9:41 AM kutsc...

From http://dx.doi.org/10.1073/pnas.1419161111 > Given the effective lengths (ie, the number of

There are no reads supporting any of the events in that file. The IJC and SJC columns are all 0,0,0,0

Got it. Thank you, Eric. On Wed, 23 Oct 2024 at 21:20, kutsc...@gmail.com <kutsc...@gmail.com