dms-vep / dms-vep-pipeline

Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)
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Accommodate multiple options for neut_std_barcode source #141

Closed fwelsh closed 1 year ago

fwelsh commented 1 year ago

Tests of the exogenous RNA spike-in standard look very promising so far. My plan is to continue using H6 as the standard for potent samples that do not neutralize H6 at selection concentrations. For less potent samples, I will normalize using this spike-in control.

It would be helpful to have an option for multiple labeled neutralization_standard_barcodes.csv inputs (or a single file, with labeled sets of barcodes for different standards). Then, in the barcode_runs.csv input, we can add an optional column to specify which neut standard that sample should be normalized against.

I've only tested the RNA spike-in against a single serum, and results were very promising but not conclusive yet. I'm getting data back tonight from a followup run where I tested the RNA spike-in standard with 5 different sera, which should provide more definitive results. But just wanted to put this on your radar for now @jbloom

jbloom commented 1 year ago

I will work on this!

jbloom commented 1 year ago

@fwelsh, you can do this. Please see the explanation in #143 for details.