In silico combinatorial peptide pooling assays

Details of the pipeline are described in the methods section of the «Identification of Antigen-Specific T Cell1 Receptors with Combinatorial Peptide Pooling»

This is snakemake pipeline with three steps.

1. Generation of CPP scheme and pooling peptides with entered parameters.

   • n_pools, number of pools
   • len_lst, number of peptides
   • overlap, shift between two overlapping peptides
   • ep_length, epitope length
   • pep_length, peptide length
   • n_proteins, number of proteins from which peptides are generated

2. Simulation of activation signal.

   
   • mu_off, $mu_{signal}$ for positive distribution
   • sigma_off, $sigma_{signal}$ for positive distribution
   • sigma_p_r, $sigma$ between replicates in positive pools
   • sigma_n_r, $sigma$ between replicates in negative pools
   • low_offset, scaling factor
   • mu_n, $mu_{neg}$ for negative distribution
   • sigma_n, $mu_{neg}$ for negative distribution
   • r, number of replicates
   • error, number of experimental errors (erroneously non-activated pools), if =100 => then all pools were non-activated

3. Activation model.