MultiRepMacsChIPSeq - generate_mean_bedGraph

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generate_mean_bedGraph.pl

A script to generate a chromosomal mean coverage bedGraph track to be used in Macs2 as the global control track when there is no input for generating a control_lambda chromatin bias track. This uses a bigWig or bedGraph coverage file to calculate a global mean. Intervals without coverage are not included in the calculation. It will write out a simple bedGraph representing the genome with the respective mean for each chromosome.

Provide an input file in either bigWig or bedGraph format.

USAGE:

generate_mean_bedGraph.pl -i file.bw -o mean.bdg

OPTIONS:

-i --in <file>      The input bigWig or bedGraph file
-o --out <file>     The output bedGraph file (input.global_mean.bdg)
-h --help           Display help