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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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I tried to merge genes with overlapping regions using agat_sp_fix_overlaping_genes.pl but it failed because their CDSs don't overlap, is there any way to fix this? Thanks!
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**Describe the bug**
I am getting Undefined subroutine error messages after running agat_convert_sp_gff2gtf.pl.
**General (please complete the following information):**
- AGAT version: 1.2.0…
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**Describe the bug**
We are trying to run AGAT which is built with Perl 5.36 and more recent Perl packages, but we are getting `Undefined subroutine` error messages.
We did the same tests with AGAT(…
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Hi, thank you for the tool, I am very excited to try it and compare the results from liftoff.
However, I am getting a gffutils error at the stage after miniprot:
```
>> Creating liftoff annotati…
jolbi updated
4 weeks ago
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Hi Jacques,
Instead of providing the average for a lot of features, can you provide the median, 90% and 95% percentile values? I feel these metrics summarize the annotation data better than average…
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The text 'Glean Bhríde' has recently gone missing in the timetable, even after a complete re-install.
Did this upload?
![Screenshot_20240530-161711](https://github.com/thecosmicfrog/LuasataGlance/…
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**Describe the bug**
According to [the documentation](https://agat.readthedocs.io/en/latest/tools/agat_sp_extract_sequences.html#agat-sp-extract-sequences-pl), the headers created by the script are f…
jdcla updated
1 month ago
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We have a lot of modules that are not managed by nf-core. It would be nice to have them managed by nf-core.
- modules/local/agat/extractsequences.nf
- modules/local/agat/filterbyattribute.nf
- mo…
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**Describe the bug**
agat_convert_mfannot2gff.pl
The feature starts from the very beginning of the mfannot file (position 1) is converted to position 2 in the generated gff.
**General (please co…