bigWigSummary

Category

BigWig Manipulation

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Usage

bigWigSummary [options] file.bigWig chrom start end dataPoints

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Manual

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

Get summary data from bigWig for indicated region, broken into dataPoints equal parts. (Use dataPoints=1 for simple summary.)

NOTE: start and end coordinates are in BED format (0-based)

Required arguments

• file.bigWig: Input bigwig file
• chrom: chromosome/contig
• start: start position
• end: end position
• dataPoints: number of bins for calculating the summary statistics

Options

• -type=X: type of the summary statistics you want to calculate, must be one of:
  • mean: average value in region (default)
  • min: minimum value in region
  • max: maximum value in region
  • std: standard deviation in region
  • coverage: % of region that is covered
• -udcDir=/dir/to/cache: place to put cache for remote bigBed/bigWigs

Example

Divide the genomic region chr8:127955641-127965435 (chrom:start-end) into 10 bins (dataPoints), and calculate the mean values (defined by -type) in each of these bins for the signals stored in the bigWig file (K562.bigWig):

$ bigWigSummary K562.bigWig chr8 127955641 127965435 10
0.066161    0.0598106    0.196098    0.281279    2.6943    2.31408    0.231602    0.129045    0.155618    0.151627

File formats this tool works with

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