bigWigCorrelate

Reference Code backup Executable files

Correlate bigWig files, optionally only on target regions.

Category

BigWig Manipulation

Usage

bigWigCorrelate [options] a.bigWig b.bigWig

Manual

This tool is part of UCSC Genome Browser's utilities.

This tool calculates basepair-wise Pearson's correlation coefficient among genomic regions. By default, it considers loci where at least one souce have non-missing values.

Required arguments

  • Choice 1: Compare two bigWig files
    • a.bigWig: input file 1
    • b.bigWig: input file 2
  • Choice 2: Compare multiple bigWig files which paths are stored in a text file. This choice is available to versions released after July 29, 2014.
    • listOfFiles: A text file with one column describing paths to all the bigWig files you want to compare. wigCorrelate has similar functionality and takes file paths directly through the command line interface.

Options

  • -restrict=restrict.bigBed: restrict correlation to parts covered by this bigBed file. If your regions are defined in bed format, please refer to bedToBigBed for instructions on format conversion. This option is available to versions released after May 25, 2013.
  • -threshold=N.N: clip values to this threshold. If set, signal values will be replaced with $\min(\text{original value}, \text{threshold})$.
  • -rootNames: if set just report the root (minus directory and suffix) of file names when using listOfFiles. This option is available to versions released after August 26, 2014.
  • -ignoreMissing: if set do not correlate where either side is missing data. Normally missing data is treated as zeros. This option is only available to versions released after August 1, 2016 ($\ge357$).

Notes

If you want to have more control on how the correlation coefficients are calculated (pearson vs. spearman, raw scale vs log scale), you can consider using the combination of multiBigWigSummary and plotCorrelation from the deeptools suite.

Examples

Calculate the correlation (Pearson's R) between two bigwig files:

$ bigWigCorrelate K562.bigWig GM12878.bigWig
0.52383

Using wigCorrelate gives identical results:

$ wigCorrelate K562.bigWig GM12878.bigWig
K562.bigWig    GM12878.bigWig    0.52383

File formats this tool works with
bigWig

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