Peak calling by Sparse Enrichment Analysis for CUT&RUN (SEACR)

Target data bedgraph file in UCSC bedgraph format that omits regions containing 0 signal.
Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
A numeric threshold n between 0 and 1 returns the top n fraction of peaks based on total signal within peaks.
“norm” denotes normalization of control to target data, “non” skips this behavior. "norm" is recommended unless experimental and control data are already rigorously normalized to each other (e.g. via spike-in).
“relaxed” uses a total signal threshold between the knee and peak of the total signal curve, and corresponds to the “relaxed” mode described in the text, whereas “stringent” uses the peak of the curve, and corresponds to “stringent” mode.
Generated output file(s) will begin with the prefix you specify.


If you use SEACR in your work, please cite Meers, MP, Tenenbaum, D and Henikoff S (2019). Peak calling by sparse enrichment analysis for CUT&RUN chromatin profiling. Epigenetics & Chromatin 2019 12:42.