bigBedSummary manual with usage examples

Usage

bigBedSummary file.bb chrom start end dataPoints

Manual

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

Required Arguments

file.bb: Path to the bigBed file containing genomic data.
chrom: Chromosome or sequence name.
start: Start position of the region.
end: End position of the region.
dataPoints: Number of data points to break the region into. Use 1 for simple summary.

Options

-type string: Type of summary to calculate. Options:
- coverage (default): Percentage of the region covered by data.
- mean: Average depth of the covered regions.
- min: Minimum depth of the covered regions.
- max: Maximum depth of the covered regions.
-fields: Print information about the fields in the bigBed file. When using this option, you can omit the chrom, start, end, and dataPoints parameters.
-udcDir /dir/to/cache: Specify the directory to cache remote bigBed/bigWig files.

Examples

Get summary statistics of bigBed records in a region

By default, bigBedSummary calculates the coverage in a region, but you can change the type of statistics by changing the value of -type.

$ bigBedSummary k562.bigBed chr1 1 1000000 1
0.037555

Get fields/columns in the bigBed file

Use the -fields option to get the list of fields in the bigBed file:

$ bigBedSummary -fields k562.bigBed
9 bed definition fields, 11 total fields
	chrom	Reference sequence chromosome or scaffold
	chromStart	Start position of feature on chromosome
	chromEnd	End position of feature on chromosome
	name	Name of gene
	score	Score
	strand	+ or - for strand
	thickStart	Coding region start
	thickEnd	Coding region end
	reserved	RGB Color
	ccre	ccRE Group
	classification	Classification type

File formats this tool works with

bigBed

bigBedSummary

Category