simplify event ids for cross referencing in genome browser

[mparker2]

Hi @EduEyras,

I am trying out SUPPA for the first time and so far I am a big fan, particularly for the interpretability of the results. Something I find slightly tricky however is looking up events in IGV using the coordinate-based naming system, especially for genes which have lots of overlapping alternative sites. I think it might be easier to cross reference if events of each gene were also given a shorter unique code, which could just be an incrementing number. What do you think?

Best wishes Matt

[EduEyras]

Hi Matt,

I'm glad that you like it.

Yes, it could be generated when the events are calculated, and it would be added to the ioe to link it to the GTF.

We did not do something like that for simplicity, to avoid having too many different ID formats lying around. In principle it could be something as simple as "GeneID_e1, GeneID_e2, etc...", right?

cheers

Eduardo

On Wed, 15 Sept 2021 at 20:11, Matthew Parker @.***> wrote:

Hi @EduEyras https://github.com/EduEyras,

I am trying out SUPPA for the first time and so far I am a big fan, particularly for the interpretability of the results. Something I find slightly tricky however is looking up events in IGV using the coordinate-based naming system, especially for genes which have lots of overlapping alternative sites. I think it might be easier to cross reference if events of each gene were also given a shorter unique code, which could just be an incrementing number. What do you think?

Best wishes Matt

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/133, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKBZEIENHY3OORRIMOP3UCBWM5ANCNFSM5ECCVTXQ . 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.

-- 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

[mparker2]

Yeah exactly. I agree that simple is better, but something more human readable would also be good. I will explore the code and maybe submit a pull request for you to look at :)

[EduEyras]

Yes, no problem

I reckon that to link the info you'll need to add a column to the .ioe / .ioi file

I'd say it is better to add it at the end. Not as elegant, but potentially breaking fewer things?

Interested in knowing your thoughts

Thanks

E.

On Wed, 15 Sept 2021 at 22:06, Matthew Parker @.***> wrote:

Yeah exactly. I agree that simple is better, but something more human readable would also be good. I will explore the code and maybe submit a pull request for you to look at :)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/133#issuecomment-919960336, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7XCXPTJC2W6S7RWVTUCCD6HANCNFSM5ECCVTXQ . 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.

-- 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