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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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How to set paramaters of braker3 with large genome (~10 Gb) with highly repetitive sequence content and many ultra-long introns? #780

Open Lixx1989 opened 3 months ago

KatharinaHoff commented 3 months ago

Never tested. First, mask very well. Second, give it a test run to see whether any component dies. Team of Jill (EASEL) probably has experience (and also knows what we didn't fix). May be worth reaching out to them?

Lixx1989 commented 3 months ago

Thank you for your reply. I used default paramaters of braker3 with both RNAseq and protein evidence to annotate my softmasked genome and got about 6,5000 genes. But I used BUSCO to estimate these annotated genes with only 54.3% C. So, maybe I should set some paramaters to retain gene models with long introns.---- Replied Message ----FromKatharina @.>Date3/13/2024 @.>@.>@.>SubjectRe: [Gaius-Augustus/BRAKER] How to set paramaters of braker3 with large genome (~10 Gb) with highly repetitive sequence content and many ultra-long introns? (Issue #780)Never tested. First, mask very well. Second, give it a test run to see whether any component dies. Team of Jill (EASEL) probably has experience (and also knows what we didn't fix). May be worth reaching out to them?—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

KatharinaHoff commented 3 months ago

The first question is whether the evidence for the long introns exists/is generated.

Lixx1989 @.***> schrieb am Mi. 13. März 2024 um 07:41:

Thank you for your reply. I used default paramaters of braker3 with both RNAseq and protein evidence to annotate my softmasked genome and got about 6,5000 genes. But I used BUSCO to estimate these annotated genes with only 54.3% C. So, maybe I should set some paramaters to retain gene models with long introns.---- Replied Message ----FromKatharina @.>Date3/13/2024 @.>@.>@.>SubjectRe: [Gaius-Augustus/BRAKER] How to set paramaters of braker3 with large genome (~10 Gb) with highly repetitive sequence content and many ultra-long introns? (Issue #780)Never tested. First, mask very well. Second, give it a test run to see whether any component dies. Team of Jill (EASEL) probably has experience (and also knows what we didn't fix). May be worth reaching out to them?—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/780#issuecomment-1993672356, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JEADYILHO5CSGOJ3RTYX7YI5AVCNFSM6AAAAABETQ4I6SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJTGY3TEMZVGY . You are receiving this because you commented.Message ID: @.***>