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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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zNormalization #46

Open mniederhuber opened 1 year ago

mniederhuber commented 1 year ago

Howdy! This has been bugging me. What's the logic to z-normalize by chromosome arm and not whole genome? Was that just because it's convenient to use seqnames which split by arm?

snystrom commented 1 year ago

Hey! No, it's because there's variable coverage per arm. If you compute mean(coverage) for: dm6, [chrX, chr2, chr3, chr4], and [chrX, chr2L, chr2R, chr3R, chr3L, chr4] you'll see high variance between each.

mniederhuber commented 1 year ago

ah! good to know. Thank you!