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| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
| https://github.com/NBISweden/AGAT…
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Hi, thanks for developing this nifty tool.
https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/blob/fc1623da5df1309d2e2f0b9bb0363aaab84708f4/cat/hints_db.py#L309-L310
ou…
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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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When I ran CAT, the following error occurred. The following is the input file and code I provided. I don't know what caused this error.
I only provide hal file and second generation transcriptome dat…
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Hi,
I'm also testing the `--augustus-pb` flag. Unfortunately, I'm getting errors also here.
```
WARNING: 2020-11-24 22:56:40,525 - Due to failure we are reducing the remaining retry count of jo…
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Hi,
First, congratulations on the development of Anchorwave, it seems a great addition to the Comparative Genomics toolkit!
I have several questions, the majority linked to the "Empty CDS file f…
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- [ ] add_value > tools/add_value
- [ ] analyze_covariates > tool_collections/gatk/analyze_covariates
- [ ] annotation_profiler > tools/annotation_profiler
- [x] bamleftalign > tools/freebayes
- [x] b…
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The spec points here: https://github.com/modENCODE-DCC/validator/blob/master/new_gff_validator.pl
This is 7 year old perl code
The SO wiki has:
http://www.sequenceontology.org/so_wiki/index.php…
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I'm using BREAKER2 to generate Augustus hints from RNA and Protein alignments. I'd prefer to use these hints as the protein-to-genome alignments found by GenomeThreader (BREAKER2) are usually better t…
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Hi,
I just installed the toolkit and I tried the test to verity if everything's fine
```
luigid --background --logdir luigi_logs
luigi --module cat RunCat --hal=test_data/vertebrates.hal --ref…