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**Is your feature request related to a problem? Please describe.**
I have a set of genes and I want to filter the gff accordingly. agat_sp_filter_feature_by_attribute_value.pl only handles single com…
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Please consider supporting the pairwise mapping format of minimap2:
https://github.com/lh3/miniasm/blob/master/PAF.md#paf-a-pairwise-mapping-format
Note that minimap2 also supports outputting SAM.…
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Build keretrendszer: Maven
CI: GitHub Actions
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Some warnings like this one are thrown:
```
WARNING level1: This feature level1 is not a duplicate but has an ID already used.
/!\ AGAT might mix up the child features and create chimeric records.
…
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**Is your feature request related to a problem? Please describe.**
I am using a recent version of AGAT that I would like to cite; but I noticed that the most recent version on the Zenodo is only 1.2.…
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Hi,
I get an error while trying to run interproscan at the step "stepPantherRunHmmer3" and it seems the problem is with the HMM file.
```
[doutree@plop] input $ ml InterProScan
[doutree@plop] in…
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Hi Felix,
We've recently analysed a paired-end 150 bp RRBS dataset, which ended having insert sizes well below 100 bp. This really concerned us, because insert size is having a huge impact on the d…
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**Describe the bug**
I used the agat_sp_compare_two_annotations.pl script to compare the reference GTF with the predicted GTF of the full-length transcriptome with a view to obtaining differences in …
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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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New term request Creatine low in urine (segal_110901180359):