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Dear Bambu team,
First of all, I have to say that I really like this tool! and your guidance is very helpful!
Now, my issue: I am comparing bambu vs FLAIR using the published data in this articl…
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
Haplotype 1:
- Cercis/canadensis/genomes/ISC453364.gnm3.GWXB
- Cercis/canadensis/annotations/IS…
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[2024-10-28 04:01:14] INFO: GTDB-Tk v2.4.0
[2024-10-28 04:01:14] INFO: gtdbtk classify_wf --genome_dir new_genome_data/ --skip_ani_screen --out_dir classify_wf_out --cpus 16
[2024-10-28 04:01:14] IN…
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The URL starting with 'ftp' is no longer accessible which causes a problem in get_genome and get_annotation in genome.smk.
To specify to use the URL starting with 'http' instead of 'ftp', 'url' param…
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### Is there an existing issue for this?
- [X] I have searched the existing issues
### Have you loaded the SQANTI3.env conda environment?
- [ ] I have loaded the SQANTI3.env conda environment
### …
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### Description of the bug
I've just upgraded sarek from 3.14 to the latest version. When I run it now it crashes out almost immediately with:
`ERROR ~ Cannot invoke method startsWith() on null ob…
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Version: `isosceles v0.2.1`
Running `prepare_transcripts` with bulk ONT reads aligned to chr1 of GRCh38 with minimap2:
```
BAM
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
Haplotype 1:
- Chamaecrista/fasciculata/genomes/ISC494698.gnm1.8Q19
- Chamaecrista/fasciculata…
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Thank you for developing such an excellent tool. The paper “Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution” mentio…
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When I was running ScanNeo2, several samples encountered errors during the VEP annotation process, specifically for the main task of SNVs. The following error occurred for all of them.
localrule ann…