MultiRepMacsChIPSeq - generate_differential

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generate_differential.pl

A script to generate differential enrichment track files. These are generated from two provided bedGraph or bigWig tracks. These may be fold enrichment (e.g. log2FE) or fragment coverage tracks. This works particularly well with nucleosome fragment coverage to identify changes in nucleosome density.

Input files are first “zeroed”, where any negative scores are reset to zero (or values set to a minimum defined value), to avoid examining regions with little or no initial enrichment. A differential track is then generated by subtracting input2 from input1. Complimentary enrichment tracks are then generated from the differential track, “positive” being enriched for input1 and “negative” being enriched for input2. The original differential track may be kept if desired.

New peaks may be called from these respective enrichment tracks, if so desired. If new peaks are to be re-called, specify the minimum delta, peak length, and gap length.

NOTE: Peaks are called on given absolute thresholds and NOT statistical confidence. Care should be taken to use a reasonably confident threshold.

USAGE:

generate_differential.pl -1 <chip1.log2FE.bw> -2 <chip2.log2FE.bw>

OPTIONS:

  Required 
	-1 --in1 <file>         The bw or bdg file for ChIP-1
	-2 --in2 <file>         The bw or bdg file for ChIP-2

  Differential
	--min <float>           Set the minimum value to keep in input (0)
    --scale <float>         If necessary, optional scaling factor for RPM files
                               only used for converting input, not output
	--keepdiff              Keep the differential file

  Re-call peaks (optional)
	--delta <float>         Threshold delta score to call a peak
	--len <int>             Minimum length of peak in bp
	--gap <int>             Minimum length of gap in bp

  Paths
	--macs <path>           ($macs)
	--manwig <path>         ($manwig)
	--w2bw <path>           ($wig2bw)
	--bw2w <path>           ($bw2bdg)

  General
	--outdir <path>         Alternate output directory
	--bw                    Convert output differential files to bw
							   default true if input is bw
							   use --nobw for false
	--db <file>             Indexed database for converting to bw
							   default uses input bigWig
	--help                  Print documentation