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This is regarding a de novo genome of a plant that was assembled lately. I used AGAT's feature extraction tool, to get the gene models predicted by AUGUSTUS. The repeat-masked genome is of size 2.6gb,…
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### Feature Request
The BED file input was removed from the `Medaka` task in [December 2023](https://github.com/CDPHE-bioinformatics/CDPHE-SARS-CoV-2/commit/b52b5e3d9ea570688cb46217cc0a470a030adca8). …
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Hi, I have been trying to use 3D-function "3DMax-3Dmodeler" in the Genomeflow to visualize my hic data. I know that the input file requires a contact matrix in sparse matrix format. I was using hic-st…
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Hi Mike,
I'm a PhD student in Laura Hug's lab currently working on a side project related to constructing universal ToLs. I was following your ToL example using the universal marker gene set and no…
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### Description of the bug
This bug has been around for a while now. When Sarek encounters an error is will often issue the correct error message along with a couple of wrong error messages. The wron…
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Hi,
I am trying to execute Cactus on a set of custom newick+genome files (assembled similar to the example).
I am working on an HPC cluster with PBS PRO and not SLURM is there any way to execute the…
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Hi there,
I am using Hifiasm (version 0.19.7-r598) to assemble a plant genome (2n=28) with HiFi and Hi-C data.
First, assuming it’s a diploid plant, so I run with command: `hifiasm -o OS010681.a…
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Dear developer,
I encountered an error while plotting data with the tool. The error message is: "[pafToBins] Binning PAF alignments, binsize=10000bpError in GenomicRanges::tileGenome(seqlengths = aln…
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Hello everyone,
I'm trying to use TRUST4 first time. I encountered the issue below. My command was
```
run-trust4 -b {bam_path} -f hg38_bcrtcr.fa --ref human_IMGT+C.fa --od {out_dir} -t 4
```
Th…
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Hello
I have two viral contigs of approximately 3500bp from the same region of a genome. The two contigs differ by just 1%. Virsorter is run as:
virsorter run -w test.out -i test.fa --min-length 150…