pMHC data processing

[leeanapeters]

Hi, thank you for the great package!

I have run this pipeline successfully without incorporating pMHC information but would like to add this in. I was wondering if you could provide more information as to the processing of barcoded pMHC-multimer data prior to calling cells as positive or negative based on your threshold? Do you have a script for processing at the cell and clonotype level?

Thank you!

Leeana

[sschattgen]

Hi Leeana,

Thanks for your interest in conga. The code was originally tailored to a specific dataset, but with a little modification, you should be able to apply these functions to your own data. I've added a solution I've used myself here. I want to point out one part of the code you will likely need to modify for your purposes. There is a mask that is applied in the get_tenx_agbt_pmhc_var_names that is used to distinguish pMHC vars from Totalseq and hashtag vars. The original dataset used 'Totalseq' on non-pMHC labels, but this can be modified to suit your needs here:

conga/conga/pmhc_scoring.py

Line 25 in 44b0096

not_totalseq_mask = ~raw.var_names.str.contains('TotalSeq')

Code is here:
pmhc_conga.txt