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Hi,
After getting the neoepitopes, I thought of a way to prioritize by using the availability of the allele and the binding score of the peptide with that allele as a factor. As you mentioned, you …
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Noticed some variants such as "p.W146*" in @timodonnell's neoepitope predictions.
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From @tavinathanson:
> I'm fairly unclear right now about how best, when using cohorts, to use epidisco results; for example using epidisco neoepitopes rather than https://github.com/hammerlab/cohort…
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Here's the guideline:
```
conda create -p mhcEnv python=3.6
pip install mhcflurry
pip install Biopython matplotlib requests pathos xmltodict
pip install torch torchvision
mhcflurry-downloads f…
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I'm running Vaxrank and I'm getting two errors. I'm trying to get a XLSX neoepitope report as output:
vaxrank --vcf 303Aligned.sortedByCoord.out.bam_dup.bam.vcf --bam 303Aligned.sortedByCoord.out.bam…
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@iskandr is changing a few things around. Also, his comment from before:
> My only suggestion would be to maybe increase the minimum MAPQ to 1 and if you're ultimately using the counts of neoepitopes…
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Hello, I am a CWL rookie. I want to use the Immuno.cwl to detect neoantigens. It makes me confused that (https://github.com/genome/analysis-workflows) contains too many CWL processes. Is there a descr…
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Hi Charles and Peter,
Is it possible to specify the length of the epitopes in the output from Neo? By default it is 31 for missense variants (15 aa upstream + 1 novel + 15 aa downstream). I'd like…
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Identifies fusion proteins from RNAseq and also catches expression of viral sequences:
https://github.com/ndaniel/fusioncatcher
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I'm not sure it's worth the extra complexity to filter candidate epitopes by a "self-ligandome" set of peptides. No one other than Kipp ever generated these peptide sets and no one seems to use them. …