No signficant results in rMATs but found significant results in leafcutter

[Akshaya Vs]

I am looking at alternative splicing events in Leukemia samples and found no significant events in rMATs at p.adj 0.05 cut-off but found around 300 events in leafcutter.

I am using the same samples and bams. Is there any reason explaining the drastic difference?

[kutsc...@gmail.com]

Here's a recent post investigating why a run had no splicing events. Some of the steps may work for you: https://github.com/Xinglab/rmats-turbo/issues/483

Specifically you can check the read outcomes section of the rmats stdout to see if reads were filtered for any reason. You can also try running with --statoff to see if reads are being assigned to any event

If rMATS is counting reads toward events but not calling any as significant, then you could try looking for any of the significant leafcutter events in the rMATS output when running with --statoff

Eric

[Changhe Ji]

Hi. Eric. I use the rmatssashimiplot to generate the pdf file. But everything works except with ot no pdf generated. Do you know what is the reason?thank you for your reply

kutsc...@gmail.com <kutsc...@gmail.com> 于 2025年4月23日周三 15:38写道：

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[kutsc...@gmail.com]

See these posts about missing sashimiplot pdf output files:

https://github.com/Xinglab/rmats2sashimiplot/issues/123

https://github.com/Xinglab/rmats2sashimiplot/issues/75
https://github.com/Xinglab/rmats2sashimiplot/issues/61

[Changhe Ji]

Now it works, the same code didn't work yesterday, but it works today😊

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