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comprna / SUPPA

SUPPA: Fast quantification of splicing and differential splicing
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Why this regions were not regarded as RI ? #150

Closed gouwei1 closed 1 year ago

gouwei1 commented 1 year ago

As the figure: 1

EduEyras commented 1 year ago

Hi,

thanks for the question. The default definition of RI in SUPPA is quite restrictive and it assumes one single intron:

----###-------###---- ----##########----

So these multi-intron retention are not picked up

If you use the option -b V ("variable boundary") the external boundary constraints are dropped. You can also allow some variability of the exon boundary matches with -t (please see options). That could work in this case

I hope this helps

Eduardo

On Thu, 20 Oct 2022 at 20:22, gouwei1 @.***> wrote:

As the figure: [image: 1] https://user-images.githubusercontent.com/90610419/196909435-6f78516d-d348-4f11-a82f-725116926eb4.png

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gouwei1 commented 1 year ago

That solved my problem. Thank you!