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Hi,
I ran your pipeline using MHCflurry and MHCflurry directly, on the same data
In the case of MHCflurry I used mhcflurry-predict and as input I had alleles from hlatyping nextflow pipeline (RNA) and a FASTA file from PrecisionProDB (using my VCFs as input)
How do you generate peptides from variants (or proteins) ?
I am not very familiar with this kind of analysis, and I am trying to understand all the steps involved.
Thanks
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