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Find Peaks
The utility findPeaks finds
peaks from the fold change file generated using foldChangeReadDepth
to find peaks with values less than a certain number and certain region size.
Prerequisites
1) Find the fold change using the
utility foldChangeReadDepth.
How
to run it?
Type java -jar PAVED.jar findPeaks -h to
see list of parameters
findPeaks utility takes as input three parameters 1) fold change
file in wiggle format, 2) minimum threshold value and 3) minimum region size
value
Run the utility as follows:
java -jar
C:\Britta\manuscript\Analysis\PAVED.jar findPeaks -i
C:\Britta\manuscript\Analysis\data\FAIRE\normalizedData\FaireRepvsInput.wig
-o
C:\Britta\manuscript\Analysis\data\FAIRE\normalizedData\FaireRepvsInput.peaks
-m 5 -n 10
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Here, "C:\Britta\manuscript\Analysis\" is the location where the jar file is present on the
local disk, -i is the fold change wiggle file, -m is the parameter
specifying minimum peak value, -n is the minimum region width and -o is
the output file with regions that are above the thresholds presented.
Sample
output
The sample
output is as follows:
This shows for example that there is a peak between 350494 and 350509 on the
chromosome LmjF05
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