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hi
I have installed agat manually from github.
Im trying to do gtf to gff3 conversion.
perl agat_convert_sp_gxf2gxf.pl -g braker.gtf -o br
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**Describe the bug**
I installed AGAT with Docker, and get normal output running ```sudo docker run quay.io/biocontainers/agat:0.8.0--pl5262hdfd78af_0 agat_sp_keep_longest_isoform.pl```
When I try…
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Good morning 😊
I am opening this issue on the recommendation of @rob-p and our discussion over on BioStar (https://www.biostars.org/p/486346/#486637).
I was using STAR to index and align my raw r…
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Is there a way to turn off the check to remove identical isoforms when running the merge two annotations?
Currently, it removing a few isoform from gencode which I believe to be not the same judin…
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Vor lezva@ntaniqine patkanum hayoc lezun?|Hndevropakan
Vortex e arajanum Agat@?|hrabxayin aparanerum
Kisatankarjeq Qar…?|Agat
trchun Jnjxukanmaneri @ntaniqic?|Agrav
Tarva mej qani angamen bazmanum agr…
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This is a pretty broad topic that's come up many times before.
In general we don't have any more real-estate to squeeze more config options in the existing Configuration GUI (aka property sheet pag…
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When indexing with tabix I get
```bash
[E::hts_idx_check_range] Region 537025265..537026246 cannot be stored in a tbi index. Try using a csi index
tbx_index_build failed: projectedGenes__Triticum_a…
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AGAT has been working great for me so far, so thanks. I'm trying to determine if the ORFs of my GTF are properly defined. Trying to work out if the start/stop codons are missing from the CDS.
I've …
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### Affected tool(s)
ConvertToRefFlat
### Affected version(s)
- [X] Latest public release version [2.5.1]
- [ ] Latest development/master branch as of [date of test?]
### Description
I am a…