How to make a custom annotation set?

[dudududu12138]

Hello,
I saw the built-in annotation file (https://github.com/Illumina/SpliceAI/blob/master/spliceai/annotations/grch38.txt). But I want to make a custom annotation set. And I want to know how did you define exons? I mean, there are more than one transcripts in some genes. And the exons may overlap. How do you deal with the situation? I list an example below :
This gene has two transcripts. Exon30976-31097 and exon 30976-31109 have the same start position but different end position.

Thank you very much for helping me!

[bw2]

You may find this script useful https://github.com/broadinstitute/SpliceAI-lookup/blob/master/annotations/convert_gtf_to_SpliceAI_annotation_input_format.py It's used for updating the annotations that underly https://spliceailookup.broadinstitute.org/

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On Tue, Jan 2, 2024, 7:10 AM dudududu12138 ***@***.***> wrote: Hello, I saw the built-in annotation file ( https://github.com/Illumina/SpliceAI/blob/master/spliceai/annotations/grch38.txt <http://url>). But I want to make a custom annotation set. And I want to know how did you define exons? I mean, there are more than one transcripts in some genes. And the exons may overlap. How do you deal with the situation? I list an example below : This gene has two transcripts. Exon<30976-31097> and exon <30976-31109> have the same start position but different end position. 1704197258038.png (view on web) <https://github.com/Illumina/SpliceAI/assets/125525648/9ec9d784-f7bb-4ebf-8d5c-17d5dbaa9398> Thank you very much for helping me! — Reply to this email directly, view it on GitHub <#143>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABPTPKTADSKXOFPKZAL5BU3YMP2KVAVCNFSM6AAAAABBJ6KD4GVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3DEMZTGI4DANA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[dudududu12138]

You may find this script useful https://github.com/broadinstitute/SpliceAI-lookup/blob/master/annotations/convert_gtf_to_SpliceAI_annotation_input_format.py It's used for updating the annotations that underly https://spliceailookup.broadinstitute.org/
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On Tue, Jan 2, 2024, 7:10 AM dudududu12138 @.> wrote: Hello, I saw the built-in annotation file ( https://github.com/Illumina/SpliceAI/blob/master/spliceai/annotations/grch38.txt http://url). But I want to make a custom annotation set. And I want to know how did you define exons? I mean, there are more than one transcripts in some genes. And the exons may overlap. How do you deal with the situation? I list an example below : This gene has two transcripts. Exon<30976-31097> and exon <30976-31109> have the same start position but different end position. 1704197258038.png (view on web) https://github.com/Illumina/SpliceAI/assets/125525648/9ec9d784-f7bb-4ebf-8d5c-17d5dbaa9398 Thank you very much for helping me! — Reply to this email directly, view it on GitHub <#143>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABPTPKTADSKXOFPKZAL5BU3YMP2KVAVCNFSM6AAAAABBJ6KD4GVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3DEMZTGI4DANA . You are receiving this because you are subscribed to this thread.Message ID: @.>

Thanks！！