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Compare bed Files Annotations
The utility compareBEDFiles
compares two bed files and outputs entries specific to the second bed file
Prerequisites
1) two bed files to be compared
How
to run it?
Type java -jar PAVED.jar compareBEDFiles -h
to see list of parameters
compareBEDFiles utility takes as input two bed files outputs the
entries specific to second bed file
Run the utility as follows:
java -jar C:\Britta\manuscript\Analysis\PAVED.jar
compareBEDFiles -i C:\Britta\manuscript\Analysis\data\MNAse\normalizedData\NakedDnaVsSheared.valleys
-j
C:\Britta\manuscript\Analysis\data\MNAse\normalizedData\MNAseChrVsSheared.valleys
-o
C:\Britta\manuscript\Analysis\data\MNAse\normalizedData\MNAseSpecific.valleys
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Here, "C:\Britta\manuscript\Analysis\" is the location where the
jar file is present on the local disk, -i and -j are the two bed
files to be compared and -o is the output file with entries specific to
file specified in -j . The output is also in .bed format
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