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Many lines are missing and some canonical genes now are classified as "RNA".
- AGAT version (v1.4.0)
- AGAT installation/use [Conda]
- OS: [Ubuntu]
I wanted to fix the gtf file that I received…
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Native AUGUSTUS GFF3 format is lacking correct unique ID= field for CDS features (they should have an incremented number for each gene), most other features except gene, transcript and CDS completely …
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**Describe the bug**
Hi,
I am unable to run the desired agat script that I want to: /agat_convert_sp_gff2gtf.pl
This could mean that agat is not succesfully installed or something in my work envi…
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Hi,
I am planning to merge GALBA result together with BRARKER3 by TSEBRA.
However, while running the standalone version of GALBA v1.0.11, I encountered an issue with five duplicated transcript ID…
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The "make test" shows two failed tests.
```
$ make test
Skip blib/lib/auto/share/dist/AGAT/so.obo (unchanged)
Skip blib/lib/auto/share/dist/AGAT/agat_config.yaml (unchanged)
Skip blib/lib/aut…
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Hello,
I received a following error while converting gtf to gff3. Kindly suggest
agat_convert_sp_gxf2gxf.pl -g input.gtf > output.gff3
Error;
EXCEPTION: Bio::Root::Exception -------------
MS…
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Hi! I am having some problems with phobius annotation
**Are you using the latest release?**
funannotate v1.8.9
**Describe the bug**
When I am trying to annotate the proteins obtained after f…
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Hi tseemann,
Thanks for the great tool. I am experiencing an issue with validating files for submission to ENA after conversion with EMBLmyGFF3 which seems to be related to an issue in the output g…
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
- Acacia/crassicarpa/genomes/Acra3RX.gnm1.YX4L
- Acacia/crassicarpa/annotations/Acra3RX.gnm1.ann…
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INFO @ Wed, 11 Sep 2024 16:26:23: Processing GTF files ...
INFO @ Wed, 11 Sep 2024 16:26:23: Building gene index .......
100000 GTF lines processed.
200000 GTF lines processed.
300000 GTF…