bigBedToBed

Category

Format Conversion

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Usage

bigBedToBed [options] input.bb output.bed

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Manual

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

Required arguments

• input.bb str: Input bigBed file.
• output.bed str: Save the converted content to this file. Specify stdout here if you want to use the output in pipeline or redirection.

Options

• -chrom=chr1: if set restrict output to given chromosome
• -start=N: if set, restrict output to only that over start
• -end=N: if set, restict output to only that under end
• -maxItems=N: if set, restrict output to first N items
• -udcDir=/dir/to/cache: place to put cache for remote bigBed/bigWigs

Example

Convert records in bigBed format into a bed file

$ bigBedToBed JASPAR2022_hg38.bb JASPAR2022_hg38.bed

Print bigBed records to the terminal

$ bigBedToBed GM12878.bigBed stdout | head
chr1    10033    10250    EH38E2776516    0    .    10033    10250    225,225,225    Low-DNase    All-data/Full-classification
chr1    10385    10713    EH38E2776517    0    .    10385    10713    225,225,225    Low-DNase    All-data/Full-classification
chr1    16097    16381    EH38E3951272    0    .    16097    16381    225,225,225    Low-DNase    All-data/Full-classification
chr1    17343    17642    EH38E3951273    0    .    17343    17642    225,225,225    Low-DNase    All-data/Full-classification
chr1    29320    29517    EH38E3951274    0    .    29320    29517    225,225,225    Low-DNase    All-data/Full-classification
chr1    66350    66509    EH38E3951275    0    .    66350    66509    225,225,225    Low-DNase    All-data/Full-classification
chr1    78990    79238    EH38E3951276    0    .    78990    79238    225,225,225    Low-DNase    All-data/Full-classification
chr1    79304    79545    EH38E2776519    0    .    79304    79545    225,225,225    Low-DNase    All-data/Full-classification
chr1    91087    91426    EH38E3951277    0    .    91087    91426    225,225,225    Low-DNase    All-data/Full-classification
chr1    98867    99117    EH38E3951278    0    .    98867    99117    225,225,225    Low-DNase    All-data/Full-classification

File formats this tool works with

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