| CUT&RUN is an efficient epigenome profiling method that identifies sites of DNA binding protein enrichment genome-wide with high signal to noise and low sequencing requirements. Currently, the analysis of CUT&RUN data is complicated by its exceptionally low background, which renders programs designed for analysis of ChIP-seq data vulnerable to oversensitivity in identifying sites of protein binding. Here we introduce Sparse Enrichment Analysis for CUT&RUN (SEACR), an analysis strategy that uses the global distribution of background signal to calibrate a simple threshold for peak calling. SEACR discriminates between true and false-positive peaks with near-perfect specificity from gold standard CUT&RUN datasets and efficiently identifies enriched regions for several different protein targets. SEACR is a highly selective peak caller that definitively validates the accuracy of CUT&RUN for datasets with known true negatives. Its ease of use and performance in comparison with existing peak calling strategies make it an ideal choice for analyzing CUT&RUN data. |
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/seacr
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| for sparse enrichment analysis | 1.3+galaxy1 | 16.01 | |