MACS2 bdgcmp

 Deduct noise by comparing two signal tracks in bedGraph (Galaxy Version 2.1.1.20160309.0)

Tool Parameters

Please provide a value for this option.
* required
Parameter 'infile_control': specify a dataset of the required format / build for parameter
* required
Method to use while calculating a score in any bin by comparing treatment value and control value
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).

Additional Options

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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.

Citations
Requirements See details
- macs2 (Version 2.1.1.20160309)
- r-base (Version 3.4)

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