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Find the Fold Change Values
The utility foldChangeReadDepth
takes as input two coverage files and finds fold changes between them
Prerequisites
1) Find the coverage using one of
the utilities findFragmentDepth or findReadDepth
for both the control and experimental datasets
How
to run it?
Type java -jar PAVED.jar foldChangeReadDepth -h
to see list of parameters
foldChangeReadDepth utility takes as input two coverage files and
generates a file containing fold change values in wiggle format.
Run the utility as follows:
java
-jar C:\Britta\manuscript\Analysis\PAVED.jar foldChangeReadDepth
-i
C:\Britta\manuscript\Analysis\data\FAIRE\normalizedData\FAIREinputChr5PCRDuplRemFilteredNorm.depth
-j
C:\Britta\manuscript\Analysis\data\FAIRE\FAIRErep2Chr5PCRDuplRemFiltered.depth
-o
C:\Britta\manuscript\Analysis\data\FAIRE\normalizedData\FaireRepvsInput
-k 0
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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 coverage file (control), -j
is the coverage
file (experimental), -k is the flag that should be set to 0 if you
intend to find peaks and to 1 if you intend to find valleys and -o is the output fold change file in wiggle
format.
Sample
output
The sample
output is as follows:
Line 1 contains a header followed by
fold change values at each of the base positions. The positions where the
denominator is zero, a character "a" is placed. To load it into IGV, replace
"a" by 0.
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