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Hi,
Is it possible to use cnvnator for analyzing datasets where the reference genome is not in the list of valid genomes (NCBI36, hg18, GRCh37, hg19, mm9, hg38, GRCh38)?
When I tried it with ba…
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I have deployed the latest version of this workflow (v2.1.2) and only adjusted the config files. I use the ENSEMBL GRCm38 mouse reference genome (release 102).
Unfortunately, the mapping step fails…
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Dear Haplomerger2 developer,
I'm very happiness to find your nice software and paper.
In my own work, i have one question about the 'heterozygous' definition. For now, I have assembled…
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Hi,
I am working on using FREEC to call CNVs in a triploid organism and was wondering if the "ploidy" variable refers to both the expected ploidy of the control and sample or just the sample (it appe…
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I am trying to convert hdf5 file into tsv file. I am giving the basic command that is suggested in the usage but I am getting this error. Can you figure out why? I am trying to convert hdf5 files from…
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Hi there!
I was looking for some feedback using wfmash to align some large (>6gb) plant genomes that are super repeat-dense, around 90%. I was able to make an alignment between species successfully (…
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Checkm2 quality report can be used. You will need to convert the Checkm2 quality report to a .csv file using:
`awk -F'\t' 'BEGIN {OFS=","} {print $1, $2, $3}' quality_report.tsv > new_file_name.cs…
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Hi, thanks for developing and updating epic2.
I wanted to see what other built-in genomes available in epic2 but can't find the list.
For example, does it have TAIR10 (Arabidopsis) genome? If so…
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Hello, i tried installing the nodejs dependencies with:
`npm install`
I get:
```
npm WARN ERESOLVE overriding peer dependency
npm WARN ERESOLVE overriding peer dependency
npm WARN ERESOLVE overr…
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Hi @tseemann, I see you posting often on this github, so thought I'd ask!
I'm having some issues getting a core genome alignment of around 300 full-length _E.coli_ sequences w/ ROARY.
The prog…