This repository implements the analysis of putative proteolytic peptides of Hoenisch-Gravel et al. (DOI). The full description of the method has been published by Fritsche et al. and was applied in this notebook.
The input data needs to have 4 columns: Sample, sequence, Uniprot, best score_netmhcpan-4.1.
The best netmhcpan score is equivalent to the best netmhcpan rank of the peptide.
HLA binding predictions were performed using the nf-core/epitopeprediction pipeline.
Lastly, a reference proteome in fasta format is required.