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snystrom / cutNrun-pipeline

Analysis pipeline for CUT&RUN Data. Currently configured for use in the McKay Lab at UNC, but extensible elsewhere by changing configuration files.
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Allow sample-specific negative control #31

Open snystrom opened 4 years ago

snystrom commented 4 years ago

Do something like:

control = lambda wildcards: sampleInfo[sampleInfo.sample == wildcards.sample].control

Maybe (pseudocode):

control_or_default(wildcards, default = CtrlPath):
    sampleInfo[sampleInfo.sample == wildcards.sample].control
    else CtrlPath
snystrom commented 3 years ago

Consider something like 2 columns: is_control_id = name or NA (if name, that name = control ID) control_sample = name or NA (if name, must be name from is_control_id, that set of samples will be pooled & used as control set)

Then have conditional peak call rules to have discriminative calling step.

Also consider whether peak calls should be made with & without control for additional comparison. Each of these new files gets added to sampleSheet.tsv