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Hello.
My name is Andrea Aguado and I am a bioinformatician currently woriking in viral quasispecies detection and further analysis. My problem resides in the VERSO step 2 inputs, since I do not k…
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Hi
I have been trying to use roberta-med for fillmask
`
nlp = pipeline("fill-mask", model="allenai/biomed_roberta_base", tokenizer="allenai/biomed_roberta_base")`
However , I get this
**Model …
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Hi,
is there any way to generate haplotype from assembled reads using cliqueSNV
Thanks
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I'm trying to reconstruct viral strains from pooled samples. I'm using `GAEseq_viral.py`.
The config included with `GAEseq_haplo.py` recommends to set the `SNP_thres` to "0.5 / ploidy for haplotype a…
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It seems that 95% of my runtime on my (viral) application is in this step. The number of vertices is pretty small usually (thousands). But it can take tens of minutes. Coverage is high, so perhaps thi…
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The `ExtractMatrix` script seems to be unable to parse SAM files properly. Neither any of my own files nor the example file.
My files
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Let's start with one of my samples. It was mapped to re…
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I've read aBayesQR and TenSQR papers. My understanding is that the MEC improvement threshold (`eta`) should be calculated for each population being analyzed. However, I see people using the values fou…
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I have generated a vcf from my bam file. for one position this is the vcf profile:
Reference 3315 . A G 111.008 . DP=4083;VDB=0.982276;SGB=-0.693147;RPB=0.00428885;MQB=1…
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- Repository: https://github.com/VHIRHepatiques/QSutils
- [X] I understand that by submitting my package to _Bioconductor_,
the package source and all review commentary are visible to the
gen…