|
Tag low coverage regions
The utility filterOutLowReadDepth tags low coverage areas depending on the average coverage of that chromosome
Prerequisites
1) .depth file generated using findReadDepth or findFragmentDepth utility in PAVED 2) Average coverage value per chromosome generated using findAverageCoveragePerChromosome utility in PAVED
How
to run it?
Type java -jar PAVED.jar filterOutLowReadDepth -h
to see list of parameters
filterOutLowReadDepth takes as input a .depth file and average coverage per chromosome file to tag low coverage regions
Run the utility as follows:
java -jar C:\Britta\manuscript\Analysis\PAVED.jar filterOutLowReadDepth -i C:\Britta\manuscript\Analysis\data\MNAse\normalizedData\MNAseRep2Chr5.depth
-o C:\Britta\manuscript\Analysis\data\MNAse\normalizedDataMNAseRep2Chr5Filtered.depth -j C:\Britta\manuscript\Analysis\data\MNAse\normalizedDataMNAseRep2Chr5Filtered.AvgCov -m 0.2
|
Here, "C:\Britta\manuscript\Analysis\" is the location where the
jar file is present on the local disk, -i is the input depth file, -j
is the average coverage per chromosome file and -o is the output file
with low coverage regions tagged and -m is the factor that determines
low coverage regions (eg. -m 0.2 selects all regions with coverage less
than 0.2*average coverage of that chromosome and tags them as low
coverage regions)
| 
