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mRNA methylation is now gone, but it seems odd that we have the other methylation terms.
@pgaudet Should this branch have "do not annotate" added, pending obsoletion?
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I am running through the example use case for annotation and none of the RNAs are getting annotated.
This is the command I am using: COMPSRA % java -jar COMPSRA.jar -ref hg38 -ann -ac 1,2,3,4,5,6 -…
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Hello,
I have assembled a mitogenome with mitoHiFi using a reference genome from a closely related species, starting from Hifiasm contigs, I could get the final.mitogenome.fasta , then I remapped H…
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FB:FBgn0031604 Elp3
elongator is no longer thought to be a histone acetyltransferase:
Elp3 Elongator complex protein 3 histone acetylation FlyBase Drosophila melanogaster IMP protein FB:FB…
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Going forward, I will add problems to this Googlesheet:
https://docs.google.com/spreadsheets/d/1AME11i0L9TtGqMINUECFKgchKfZWNdk7RvaGM6VyeBY/edit#gid=0
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Please provide as much information as you can:
* **GO term ID and Label**
GO:0065009 "regulation of molecular function"
* **Reason for deprecation**
We have discussed that this term an…
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Most of the tRNAs have no products
http://japonicusdb.kmr.nz/results/from/id/3d8939a6-271b-49c3-84fd-c348f127c5ed
Are these missing from the gff file? If so I suggest for now that we just stic…
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Dear Rémi,
These are rather general question but I think this is still the best channel to ask them since you were very helpful with a previous inquiry of mine.
I used the following array script t…
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Hello. I installed gffread 0.12.1 through anaconda and used to convert a GFF3 file into GTF format.
The file I used is the gff3 annotation file from Araport11:
[https://www.arabidopsis.org/download_…
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For input:
1. I have got a GFF file from PlasmoDB. "PlasmoDB-66_PvivaxP01.gff"
2. I converted it to GTF file using agat `agat_convert_sp_gff2gtf.pl --gff ../PlasmoDB-66_PvivaxP01.gff -o PlasmoDB-66_…