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BRAKER3 worked for several genomes, but did not for a genome. As shown below, the error occurred as described in the title.
```
singularity exec -B /ddn:/ddn /app/centos8/braker/braker-20230308/br…
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It only supports hg38 and mm10 by default. We may need to reach out to the Arriba maintainer for help creating these fusion files for other genome annotations.
https://github.com/CCBR/RENEE/blob/5f…
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### Feature Request ✨
GenBank doesn't have an RSV template so we will need to create the GFF file to submit.
### Solution 💡
We can use VADR's RSV model to generate which produces a genome ann…
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Hello,
Thanks for the tool. I successfully went through your test files.
I'm trying to generate an optimized annotation for ensembl's latest mm39 annotation and am running into an error during…
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Hi,
I want to convert the Prodigal output to standard GFF3 using the command: convert_prodigal_to_gff3.py -i unit2_new_genome.prodigal.gff -o unit2_new_genome.prodigal.gff3
I obtain this error …
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Hi there!
I have tried multiple ways including running the docker version of blast and every time I am not able to complete the blast run. It probably is something I am doing differently, but I am …
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### Aims/objectives.
What if we use *e.g.* Ensembl 110 (for sequence context, annotation in general such as features, gene assigment, and complementing RBP annotation) and link reported sites to Ense…
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Hello,
I want to run core gene analysis with Spine locally and also want to include gff file, I use -f for genome_files.txt which containing paths to fasta file and their coresponding gff files. It i…
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Dear Author,
Thanks for developing this nice tool!
I have some questions regarding to your local assembly steps:
1. How do you extract the flanking sequence from reference? Is that based on th…
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Hi All,
today while running the following [GTN tutorial](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html), we discovered …