Hi-C analysis
What is the input file required to find the correlation difference between 2 experiments using getHiCcorrDiff.pl script?
getHiCcorrDiff.pl <outputPrefix> <HiC Tag Directory1> <HiC Tag Directory2>
This command is given in the documentation. What are HiC Tag Directory1 and HiC Tag Directory2 explicitly and what information does it have?
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Did you see this: http://homer.ucsd.edu/homer/ngs/tagDir.html