Category
Genomic Interval Manipulation
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
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