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Function: MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
Usage: macs2 [-h] [--version] {callpeak,filterdup,bdgpeakcall,bdgcmp,randsample,bdgdiff,bdgbroadcall}
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Function: Normalize the scores of two bigWig files to each other (e.g., ratios)
Usage: bigwigCompare --outFileName FILENAME --bigwig1 BigWigFile1 --bigwig2 BigWigFile2 [options]
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Function: 1. Delineation of the significantly ChIP-enriched regions, which can be used to associate with other genomic landmarks. 2. Identification of reads on the ChIP-enriched regions, which can be used for profiling and other quantitative analysis.
Usage: sh DIR/SICER.sh ["InputDir"] ["bed file"] ["control file"] ["OutputDir"] ["Species"] ["redundancy threshold"] ["window size (bp)"] ["fragment size"] ["effective genome fraction"] ["gap size (bp)"] ["FDR"]
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Function: MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing differential binding events between conditions.
Usage: java -Xmx20G -jar multigps.jar <options - see below>