Comments (5)
ifiddes
commented on August 13, 2024
Hmm, that is definitely a bug. The --assembly-hub flag will possibly help you in that it will produce a bigBed of the annotation set (unsure if Apollo supports bigBed, never used it).
As a temporary workaround, you should be able to convert the genePred annotation set to BED using the genePredToBed tool that you have (CAT requires it). I assume Apollo supports regular BED. But obviously, you will lose all of the extra names and tags.
I will figure out why the GFF3 output is invalid.
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ifiddes
commented on August 13, 2024
That was an easy fix, actually. Commit 5cbee6e.
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lassancejm
commented on August 13, 2024
👍 Apollo does support regular Bed for sure, but it is nice to be able to keep all the extra info available from the gff format. Made the change in my local distro, had relaunched the pipeline with the --assembly-hub flag, so I have to wait a bit before closing this.
Will keep you update, but I suspect things will be good with your correction.
Thanks!
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ifiddes
commented on August 13, 2024
You will need to run with the --rebuild-consensus flag to rebuild the GFF3
with the bug fix.
On Thu, Apr 13, 2017 at 9:17 AM lassancejm ***@***.***> wrote:
👍 Apollo does support regular Bed for sure, but it is nice to be able to
keep all the extra info available from the gff format. Made the change in
my local distro, had relaunched the pipeline with the --assembly-hub flag,
so I have to wait a bit before closing this.
Will keep you update, but I suspect things will be good with your
correction.
Thanks!
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UC Santa Cruz Genomics Institute
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lassancejm
commented on August 13, 2024
As expected, the bug fix did the trick! Closing now.
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