How do I run the TiMAT2 CorrelationMap application on chIP-chip promoter array data?

Here's an example: #Make all of the possible intervals from a T2 run serialized window file java -jar -Xmx1000M ~/Apps/IntervalMaker -s -50 -i 1 -o 2 -g 250 -z 60 -f \ /Users/nix/HCI/PIs/Cairns/ZebraFish/Results/H3K4K27me3Combine/Win/all_Win #Make a text file containing chromosome, start, and stop for each interval, # this represents all of the interrogated promoters on the zebrafish array java -jar -Xmx1000M ~/Apps/IntervalReportPrinter -c -f \ /Users/nix/HCI/PIs/Cairns/ZebraFish/Results/H3K4K27me3Combine/Win/all_Win1Indx86672 #Find the best window within each promoter (if desired use the -m option to # find the lowest scoring window for identifying reduced regions from a diff analysis) java -jar -Xmx1000M ~/Apps/BestWindowScoreExtractor -w \ /Users/nix/HCI/PIs/Cairns/ZebraFish/Results/H3K4K27me3Combine/Win/all_Win \ -r /Users/nix/HCI/PIs/Cairns/ZebraFish/Results/H3K4K27me3Combine/Win/all_Win1Indx86672. Xls \ -z 60 -i 1 > /Users/nix/HCI/PIs/Cairns/ZebraFish/Results/ ... more.

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