Something went wrong with detection of A5 and A3

[gouwei1]

After adding -b V to command: suppa.py generateEvents, the detection of A5 went wrong as the figure shown in IGV using *_A5_variable_10.gtf. There should not be a A5, and also the position aligned to genome was not corrected (the order seems like - while it marks with +: 2533101 2532751 . +)

[gouwei1]

Detection of A3 also went wrong:

[EduEyras]

Sorry, I do not understand your question

Also, the coordinates e.g. 2533201 and 2532751 should be in the GTF as alternative 5' splice sites (the exonic position). Do you mean they are not?

E.

On Tue, 25 Oct 2022 at 23:55, gouwei1 @.***> wrote:

After adding -b V to command: suppa.py generateEvents, the detection of A5 went wrong as the figure shown in IGV using *_A5_variable_10.gtf. There should not be a A5, and also the position aligned to genome was not corrected (the order seems like - while it marks with +: 2533101 2532751 . +)

[image: 图片] https://user-images.githubusercontent.com/90610419/197776353-e5ee4f79-50be-4ec4-9019-df2060e8a8b9.png

— Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/151, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7HTTALIED7L3ESY4TWE7KCVANCNFSM6AAAAAARN6GTEY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[EduEyras]

Could you specify whether it is the coordinates of the alternative sites, or just the GTF of the events?

I cannot tell from the IGV pictures what the exon positions of the transcripts are to confirm whether the events are right or not.

E.

On Tue, 25 Oct 2022 at 23:59, gouwei1 @.***> wrote:

Detection of A3 also went wrong: [image: 图片] https://user-images.githubusercontent.com/90610419/197779312-e8c703fb-f80e-4afe-8463-29d021baf23f.png

— Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/151#issuecomment-1290514518, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKBZNNYXFTFYGW2HGM4TWE7KS5ANCNFSM6AAAAAARN6GTEY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[gouwei1]

The four transcripts above were from input GTF for splicing event detection, and below are results file *_A5_variable_10.gtf. I think there should not be a A5 or A3 (the second picture). Their positions of 5' were identical:

[EduEyras]

Thanks, so the coordinates in the event do not appear in the GTF at all? I'm wondering where those two positions in the A5 event come from in the GTF. E.

On Wed, 26 Oct 2022 at 00:27, gouwei1 @.***> wrote:

The four transcripts above were from input GTF for splicing event detection, and below are results file *_A5_variable_10.gtf. I think there should not be a A5 or A3 (the second picture). Their positions of 5' were identical: [image: 图片] https://user-images.githubusercontent.com/90610419/197785725-5310d4e7-6d43-41f4-9465-833516b8ca02.png

— Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/151#issuecomment-1290550296, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7BB7GO6YTXWXVZKR3WE7N3NANCNFSM6AAAAAARN6GTEY . You are receiving this because you commented.Message ID: @.***>

[gouwei1]

Yes, the detections of A3 or A5 seem wrong. But if I remove -b V, they can not be detected. The input and output files were sent to your e-mail (eduardo.eyras@upf.edu), and you could have a check with them.