how does whippet define exon skip events?

Question

how does whippet define exon skip events?

Opened this issue 4 years ago · 5 comments

mhjiang97 commented 4 years ago

can Whippet detect exon skip events?

it seems that CE (core exon) doesn't contain exon skip.

Thank you!

Answer 1 · 2020-12-29T02:24:01.000Z

Dear Zheng, Many thanks for the reply! Best, Minghao

…

2020年12月27日 22:48，Zheng An ***@***.***> 写道： can Whippet detect exon skip events? it seems that CE (core exon) doesn't contain exon skip. Thank you! Hi, I also noticed this and I found that if we need to calculate the number of exon skipping events, we need to check Inc_Paths and Exc_Paths in your psi file. For all CE node, we need to make sure that it occurs in Exc_Paths so we can identify this event as exon skipping event. Best, Zheng — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#107 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMUSZFP4MNK6KSE46IWYK4LSW5CM7ANCNFSM4TMEL3HQ>.

Answer 2 · 2021-01-07T14:04:28.000Z

Hi,
I am sorry - I do not see the reply but have the same question.
Thank you!

Answer 3 · 2021-01-08T06:01:22.000Z

Hi,
I am sorry - I do not see the reply but have the same question.
Thank you!

Hi,

click the button ... at the end of my reply above, and you will find Zheng's advice~

Cheers,
Minghao

Answer 4 · 2021-01-11T10:09:55.000Z

Oh, I see. Sorry. Thank you!

Answer 5 · 2024-07-15T11:41:30.000Z

I have samples in two groups: a control group and a treatment group, each containing three replicates. I am interested in identifying significant changes in exon skipping/inclusion between the control and treatment groups. Is there a way to analyze this across replicates? The method you mentioned appears to check exon skipping/inclusion events in a single replicate.

Thanks,

Xiao

Dear Zheng, Many thanks for the reply! Best, Minghao
…
2020年12月27日 22:48，Zheng An @.***> 写道： can Whippet detect exon skip events? it seems that CE (core exon) doesn't contain exon skip. Thank you! Hi, I also noticed this and I found that if we need to calculate the number of exon skipping events, we need to check Inc_Paths and Exc_Paths in your psi file. For all CE node, we need to make sure that it occurs in Exc_Paths so we can identify this event as exon skipping event. Best, Zheng — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#107 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMUSZFP4MNK6KSE46IWYK4LSW5CM7ANCNFSM4TMEL3HQ.