How to create Correlation plots between wig files

Question

[macmath]

I have two wig files and wish to perform correlation plot before merging the two files. I checked with http://cistrome.org/ for performing the needful. Was interested to know more ways to perform it.

Answer 1

[Ryan Dale]

You can use the wigToBigWig and bigWigCorrelate tools from UCSC (find the executable for your platform here).

First convert your WIG files to bigWig:

wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
   wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
options:
   -blockSize=N - Number of items to bundle in r-tree.  Default 256
   -itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
   -clip - If set just issue warning messages rather than dying if wig
                  file contains items off end of chromosome.
   -unc - If set, do not use compression.
   -fixedSummaries - If set, use a predefined sequence of summary levels.
   -keepAllChromosomes - If set, store all chromosomes in b-tree.

Then correlate them:

​bigWigCorrelate - Correlate bigWig files, optionally only on target regions.
usage:
   bigWigCorrelate a.bigWig b.bigWig
options:
   -restrict=restrict.bigBed - restrict correlation to parts covered by this file
   -threshold=N.N - clip values to this threshold

[valentina.boeva]

Does anybody have more details about how bigWigCorrelate works?