misss some alternative splice pattern

[zpliu1126]

Dear SUPPA team

when I search AS pattern By gene annotion；I find that it can't detect such RI models。

the green/red rectangle represent exons

[EduEyras]

Hi,

thanks for your message.

You are right, SUPPA only identifies single intron retention events https://github.com/comprna/SUPPA#generation-of-transcript-events-and-local-alternative-splicing-events

Even with the option for variable boundaries (-b V), it will probably only identify single intron retention events.

Are these double intron retention common in your case?

Thanks

Eduardo

On Wed, 16 Sep 2020 at 21:41, zpliu1126 [email protected] wrote:

Dear SUPPA team

when I search AS pattern By gene annotion；I find that it can't detect such RI models。 [image: image] https://user-images.githubusercontent.com/39325949/93332216-187ce100-f854-11ea-8093-425ee78bec02.png

the green/red rectangle represent exons

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/100, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKBYN3RODMR2REKE27X3SGCP6PANCNFSM4ROWIWGQ .

-- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

[zpliu1126]

Thank you for your reply。 I'm not sure how many it have。 But I find this double intron retention events in a isoform，and it will result in stop coden earlyer。

[EduEyras]

Alternatively, you can run SUPPA to study differential transcript usage (DTU). That will detect that relative change if it occurs between two or more conditions that you might be comparing. Best E.

On Wed, 16 Sep 2020 at 23:51, zpliu1126 [email protected] wrote:

Thank you for your reply。 I'm not sure how many it have。 But I find this double intron retention events in a isoform，and it will result in stop coden earlyer。

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/100#issuecomment-693419618, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB6BOTIM5VUBQYO3VNDSGC7HTANCNFSM4ROWIWGQ .

-- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ