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Hello!
I'm trying to add introns to my GFF file using the command agat_sp_add_introns.pl --gff MY.gff --out MY_introns.gff
Unfortunately, I got the below error. I also tried using the commands …
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**Describe the bug**
I installed `agat` using conda with `-c bioconda`. However, the resulting agat_sp_filter_feature_by_attribute_value.pl is an old version.
**General (please complete the follow…
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This is regarding a de novo genome of a plant that was assembled lately. I used AGAT's feature extraction tool, to get the gene models predicted by AUGUSTUS. The repeat-masked genome is of size 2.6gb,…
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| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
| https://github.com/NBISweden/AGAT…
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**Describe the bug**
When running the command, it gets towards the bottom of the process but then errors saying the it could not open the index file. This is a resulting GFF file from MAKER output.
…
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**Describe the bug**
Not sure if it is a standard behaviour, but I am trying to add missing information (e.g transcript, exon or gene) to my GTF file.
Using: `agat_convert_sp_gxf2gxf.pl --gtf $INGTF…
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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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**agat_sp_merge_annotations.pl output incompatible with cellranger**
I have two gff files I want to merge.
One is an old annotation, and the other is a new annotation I have just made using brake…
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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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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…