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MACS2 bdgcmp (version 2.2.9.1+galaxy0)
Available choices are: ppois, qpois, subtract, logFE, logLR, and slogLR. They represent Poisson Pvalue (-log10(pvalue) form) using control as lambda and treatment as observation, q-value through a BH process for poisson pvalues, subtraction from treatment, linear scale fold enrichment, log10 fold enrichment(need to set pseudocount), log10 likelihood between ChIP-enriched model and open chromatin model(need to set pseudocount), symmetric log10 likelihood between two ChIP-enrichment models, or maximum value between the two tracks. Default=ppois (--method).

What it does

This is bdgcmp utility from the MACS2 Package. It is designed to deduct noise by comparing two signal tracks in bedGraph.


Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening.