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neurogenomics / CUT_n_TAG

Preprocessing pipeline for CUT&TAG data.
MIT License
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Call consensus peaks on all our C&T samples #21

Closed bschilder closed 1 year ago

bschilder commented 2 years ago

Call consensus peaks on all our C&T samples (grouped by mark and cell line). Specifically, merge the bam files and recall peaks using SEACR and MACS2.

See here for other strategies on consensus peak calling: https://github.com/neurogenomics/TIPseq/issues/4

bschilder commented 1 year ago

Redo with more thresholds.

bschilder commented 1 year ago

Pooled peaks called with SEACR at 0.1 threshold (top 10% strongest peaks).

All samples

Includes both internal (Neurogenomics Lab) and external (previously published) bulk CUT&Tag H3K27ac samples (7 samples total). At 80% precision, recall was 64.2%

Plot

pr_pooled_allCT.pdf

Predicted recall

Image

Internal samples

Only includes internal bulk CUT&Tag H3K27ac samples (5 samples total). At 80% precision, recall was 59.6%.

Plot

pr_pooled_internalCT.pdf

Predicted recall

Image