I appreciate your good work.
Thank you very much.
Post by Nathan DunnYasuhiro,
We have created a final update for this issue with the code released in
- when using the âadd_transcripts_from_gff3_to_annotations.plâ script, if
you use the -X (uppercase) option, CDSâs are imported as-is from the GFF3
(they are not recalculated). I think this is the only change you needed.
- the default behavior when creating an annotation from evidence (not using
the existing script) is to re-calculate the CDS
- to over-ride the default behavior and use evidence as-is without
apollo.use_cds_for_new_transcripts = true
Let us know you have any questions / comments or if there is a problem with this.
Thank you for bringing it to our attention,
Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
Dear Yasuhiro -
I kindly suggest that you please wait just a little longer before pulling
from master. After more discussion within the Apollo development team I made
some suggestions for corrections to the patches that were pushed today.
https://github.com/GMOD/Apollo/issues/1297
https://github.com/GMOD/Apollo/pull/1298
https://github.com/GMOD/Apollo/pull/1299
We will be able to get back to this tomorrow morning (US West Coast and
Midwest Time zones).
We are working furiously on it, and will update as soon as it is ready.
Thanks again.
cheers,
~moni.
Post by éæ¨åº·æ´Thank you.
That helps me a lot.
Yasuhiro
Post by Nathan DunnThis is fixed and in master now (thanks Deepak!) if you want to re-clone or
pull you should pick it up. The default is what you want so no
configuration changes will need to be made.
Nathan
By default it should do this since the default apollo variable
âuse_cds_for_new_transcriptsâ is set to true. However, we identified a
https://github.com/GMOD/Apollo/issues/1297
We should have a fix for this relatively soon (and will repost once its merged).
Thanks for bringing it to our attention and sorry for the inconvenience.
Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
Dear Apollo team members,
I installed Apollo 2.0.4 and used
"add_transcript_from_gff3_to_annotations.pl"
script to bulk load GFF3 file.
But some loaded CDS coordinates were different from original ones.
Maybe those were recalculated.
How can I load original CDS coordinates?
Thanks,
Yasuhiro
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Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory
Lawrence Berkeley National Laboratory
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