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arefeen / TAPAS

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APA site detection beyond the 3'-UTR? #19

Open lennartraman opened 2 years ago

lennartraman commented 2 years ago

Hi devs,

First of all, thanks for TAPAS!

My question is quiet simple: can TAPAS only detect APA sites within the 3'-UTR, or can it also detect APAs more upstream (intronic/exonic)?

Thanks for your valuable insight.

Best Lennart

arefeen commented 2 years ago

Hi Lennart,

I am glad that you like TAPAS.

It can detect APA sites in 3'-UTR region. If you want to detect APA sites in intronic or exonic region please use DeepPASTA (another APA site detection tool from our lab).

Thanks, Ashraful

On Thu, Nov 4, 2021, 8:27 AM lennartraman @.***> wrote:

Hi devs,

First of all, thanks for TAPAS!

My question is quiet simple: can TAPAS only detect APA sites within the 3'-UTR, or can it also detect APAs more upstream (intronic/exonic)?

Thanks for your valuable insight.

Best Lennart

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/arefeen/TAPAS/issues/19, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACNFASEZTUG4ETWIFJZ27FDUKKQ7LANCNFSM5HLXAS3A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

lennartraman commented 2 years ago

Hi @arefeen

Thanks for your quick response! Just to be sure: DeepPASTA can detect APAs in, let's say, the complete gene, based on mRNA sequencing data as input?

Thanks a lot, Lennart

arefeen commented 2 years ago

Yes, that's right. Please read the webpage of DeepPASTA for more information.

On Thu, Nov 4, 2021, 9:09 AM lennartraman @.***> wrote:

Hi @arefeen https://github.com/arefeen

Thanks for your quick response! Just to be sure: DeepPASTA can detect APAs in, let's say, the complete gene, based on mRNA sequencing data as input?

Thanks a lot, Lennart

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/arefeen/TAPAS/issues/19#issuecomment-961191685, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACNFASHCM3M6FJYISKUDCKDUKKV2NANCNFSM5HLXAS3A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

lennartraman commented 2 years ago

Alright, thanks a lot!