epitopeprediction using mhcflurry vs running directly mhcflurry

[gianfilippo]

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