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dms-vep / flu_h3_hk19_dms

Analysis of a multi-mutant, barcoded influenza H3 library in the A/HongKong/45/2019 background.
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Pipeline outputs empty file for `results/func_scores/functional_selections.csv` #42

Closed fwelsh closed 6 months ago

fwelsh commented 1 year ago

Currently, running dms-vep-pipeline (version 2) doesn't return any functional scores for my data. As far as I can tell, I have the correct parameters set up in config.yaml. I think the error occurs in line 24 of func_scores.smk, in the function get_functional_selections(barcode_runs). The output file results/func_scores/functional_selections.csv is generated, but does not have any entries.

I haven't been able to figure out the source of this error, @jbloom when you have time could you help troubleshoot?

jbloom commented 1 year ago

@fwelsh, the reason for this is you don't have the data entered to compute functional scores.

That can be done if you have both an infection without antibody (eg, no-antibody_control sample type), and also some sample from prior to selection (in your case, this would probably be plasmid sample type) in your barcode runs file.

Right now you have the no-antibody control, but not the plasmid samples. Do you have runs from sequencing your plasmid barcodes that could be added?