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Find Valleys
The utility findValleys finds
valleys from the fold change file generated using foldChangeReadDepth
to find valleys 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 findValleys -h
to see list of parameters
findValleys 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 findValleys -i
C:\Britta\manuscript\Analysis\MNAse\normalizedData\MNAseChrVsSheared.wig -o
C:\Britta\manuscript\Analysis\MNAse\normalizedData\MNAseChrVsSheared.valleys
-m 0.2 -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 depth of the valley, -n is the minimum region width covering
the valley 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 valley between 351278 and 351294 on the
chromosome LmjF05.
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