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Hello VG team,
Thank you very much for your support and I apologize if this is not the right place to ask for help.
I am trying to genotype some variants using vg autoindex + giraffe + pack + ca…
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Hi!
I'm using RESPECT to evaluate 10 octopus genomes - genomes that are expected to be human-sized or larger and repeat rich. Years ago people thought the genomes would be duplicated - but this has…
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**Overall question**
I was wondering about model choice (i.e., haplotypes, transcripts, or haplotype-transcripts).
**Model choice**
I have RNA-seq data for which the diplotype of each indivi…
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[small_test_data2.maf.gz](https://github.com/cmdcolin/mafviewer/files/10264095/small_test_data2.maf.gz)
Hello, I used the script maf2bed.pl to convert the maf file output by cactus software to bed …
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**1. What were you trying to do?**
I am trying to create an index for a gfa generated with PGGB.
**2. What did you want to happen?**
With the majority of the chromosomes I'm working with the …
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Hi there,
I am trying to run Hisat2 on FASTA files and, I've encountered an issue. It seems that HISAT2 can't read the index files, however, I'm pretty sure it's not due to typos. I have re-downloa…
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Within XBB.1.9 there appear to be 2 lineages with S:S486P:
https://next.nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_175a4_8ead10.json?branchLabel=nuc%20mutations&c=countr…
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**Description**
Hello @rpetit3 ,
We are currently using the `shigeifinder` wf in the bactopia tools, but it stucks for many hours. Please find the logs below.
> (base) gilmansiu3@gilmansiu3-Z49…
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# OGS remapping (@mpoelchau)
- [ ] request whole-genome alignment
- [ ] Set up data directories and get data
- [x] run remap-gff3
# Change old content (@mpoelchau)
- [ ] back up and deprecate…
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I'm getting an error towards the end of the pipeline.
Here's the relevant output section.
```
[2022-11-30T11:34:41-0800] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-M
ASTER: Jo…