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Hello,
I have a D.melanogaster gff3 from Ensembl and I've extracted the transcript ids of the canonical transcripts for each protein coding gene. I would like to filter (keep) all entries in the gf…
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### Solution to issue cannot be found in the documentation.
- [X] I checked the documentation.
### Issue
I used the ARM mambaforge to install mamba on my apple silicon M1.
My base environm…
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Hey,
I am getting a biotype related error:
`Runtime error:
Traceback (most recent call last):
File "/ebio/abt6_projects9/abt6_software/bin/Comparative-Annotation-Toolkit/env/local/lib/python…
fbemm updated
6 months ago
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**Describe the bug**
I was wondering if `agat_sp_fix_overlaping_genes.pl` performs similar function as [collapse_annotation.py](https://github.com/broadinstitute/gtex-pipeline/blob/master/gene_model/…
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This isn't really a bug *or* a feature request, and is related to #219. It took me a while to figure out this behavior (default table 1 allowed start codons are AUG, UUG and CUG) and that there was a …
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Hello,
I have these files in my pwd:
cd /project/PI/USERS/me/czi/data/tc/
[me@midway3-login3 tc]$ ls
agat_1.0.0--pl5321hdfd78af_0.sif
in.gff
out.gff
I installed AGAT via singularity:
…
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```ruby
# model
path = 'model/DNABERT2-117M'
config = BertConfig.from_pretrained(path)
model = AutoModel.from_pretrained(path, config=config,trust_remote_code=True)
# train
trainer = Trainer(mod…
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**Are you using the latest release?**
Yes, running 1.8.17
**Describe the bug**
When I run funannotate annotate on 2 of my 12 genomes, I immediately get the error: KeyError: 'FUN_000001' (or KeyEr…
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Hi,
I have a custom genome with a custom annotation that I'm trying to use to build my own database. But I get the following errors
```
FATAL ERROR: No CDS checked. This is might be caused by d…
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Thanks for this nice tool. I'm running into an issue trying to validate embl files that were generated on your tool. I'm using webin-cli-1.7.1 and it throws up the below error when I try to validate/s…