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**Describe the bug**
I installed all the code and perl modules for AGAT, and I am trying to run agat_sp_add_introns.pl
However, I keep on getting an error message (as seen in the screenshot attached…
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Hello,
I ran into an issue where `ch-image pull` gives an error whenever I try to run it: `error: can’t unlink: part_a91d96a12e98e16c570e2fc88a976f3a26752c3934df068a2e3ee6ffc72b43c2.tar.gz: No such…
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Combine all the output of QUAST, BUSCO and AGAT, as well as the tree in newick format from Orthofinder (ORTHOFINDER_GO)
Use the script in the additional script folder (R) to produce a plot with the…
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Hi,
I think I adjust the annotation file as required:
![image](https://github.com/zolotarovgl/GeneExt/assets/174808557/d915ba1e-2806-49ec-b1c6-8467fadd7dc1)
and I ran like this:
python geneex…
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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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Hello!
I'm having a slight issue with the annotations generated by EGAPx. When I translate the CDS into a protein sequence, I'm seeing a lot of premature stop codons. This is a species where I am s…
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Dear David,
Thank you very much for your project and support.
Does it possible to add support of AGAT 840K format?
Agat is a very common soviet computer, based on Apple II. It use to formats: App…
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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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### Description of feature
If/when we get gff-errors with featureCounts, see if the gffread-module will solve our problems, if so - implement it.
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Hi, I got my GFF file from Funannotate, and it looks like the one below. When I ran IsoQuant, it reported an error saying 'gene_id attribute value cannot be found.' Could you please give me some advic…