hg38

[herber4]

Has anyone done formatting to run suppa with the Hg38 gtf?

If so, could you throw it in a repo for us to use?

Ive yet to be able to get SUPPA to work with a Hg38 reference, only the outdated Hg19.

Best,

Austin

[EduEyras]

Hi,

SUPPA should work with any GTF and any transcriptome file associated with that GTF. It is entirely agnostic of the reference system.

We've been using SUPPA on hg38 already for a while

In which sense you have not been able to work with SUPPA on the hg38?

Eduardo

On Thu, 16 Sept 2021 at 02:32, herber4 @.***> wrote:

Has anyone done formatting to run suppa with the Hg38 gtf?

If so, could you throw it in a repo for us to use?

Ive yet to be able to get SUPPA to work with a Hg38 reference, only the outdated Hg19.

Best,

Austin

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[herber4]

I have been unable to get any PSI values when using Hg38. everything just comes out as NA.

Can you link me to the versions of the Hg38 GTF and transcripts you all have gotten to work?

Best,

Austin

[EduEyras]

Hi,

we've been using Gencode v27, v29, etc...

please send me your email and I'll put you in contact with someone from the group who could give you more specific details

E.

On Thu, 16 Sept 2021 at 21:10, herber4 @.***> wrote:

I have been unable to get any PSI values when using Hg38. everything just comes out as NA.

Can you link me to the versions of the Hg38 GTF and transcripts you all have gotten to work?

Best,

Austin

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/135#issuecomment-920806786, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKBZ7XSFARRYKHE6ZDNTUCHGC5ANCNFSM5EC3AJEQ . 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

[herber4]

herber4@clemson.edu

Thanks!

[EduEyras]

Did you solve this issue?

SUPPA only uses the "exon" lines, and it should work with standard GTF.

Did you check that the quantification file uses the same transcript IDs as in the GTF?

cheers

E.