novel AS events detection from RNA seq
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13 months ago
Sara ▴ 220

I am trying to find the Alternative Splicing events in my RNAseq data. to do so I have used both SUPPA2 and rmats but realized that both of them need gtf file (annotation file) that means using these 2 tools we can only detect annotated events. so my question is that is there any tool which can be used to detect novel events (that are not in annotation files)? can I detect the novel events using SUPPA2 and rmats?

Splicing Alternative • 599 views
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Hi Sara, as far as I know rmats can detect novel events from the reads in your BAM file, although it is still annotation-dependent. You can take a look at this an other issues in their repository. Sometimes you can find information that is not clear in the documentation. I don't know if it's the same for SUPPA2.

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13 months ago

There are a couple of alternatives to leafcutter which you can read about there.

Cheers Kristoffer

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13 months ago

Leafcutter can be used for detecting novel splicing events as claimed in their paper. The idea is to quantify intron clusters.