bedtools random

Category

Genomic Interval Manipulation

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Usage

bedtools random [OPTIONS] -g <GENOME>

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Manual

This tool is part of the bedtools suite and it's also known as randomBed.

Related tools: bedtools shuffle

Required arguments

• -g genome: The genome file should be tab-delimited and structured as follows: <chromName><TAB><chromSize>. You can get this file for the genome release that you are working with by using fetchChromSizes.

Options

• -l int: The length of the intervals to generate. Default = 100.
• -n int: The number of intervals to generate. Default = 1,000,000.
• -seed int: Supply an integer seed for the shuffling. By default, the seed is chosen automatically.

Examples

By default, bedtools random generate 1 million intervals of length 100 placed randomly in the genome specificed with -g.

$ bedtools random -g hg19.genome
chr2  87536758        87536858        1       100     -
chrX  46051735        46051835        2       100     +
chr18 5237041 5237141 3       100     -
chr12 45809998        45810098        4       100     +
chrX  42034890        42034990        5       100     -
chr10 77510935        77511035        6       100     -
chr3  39844278        39844378        7       100     -
chr6  101012700       101012800       8       100     +
chr12 38123482        38123582        9       100     +
chr7  88508598        88508698        10      100     -

$ bedtools random -g hg19.genome
chr3  141987850       141987950       1       100     +
chr5  137643331       137643431       2       100     +
chr2  155523858       155523958       3       100     -
chr5  147874094       147874194       4       100     +
chr1  71838335        71838435        5       100     -
chr8  71154323        71154423        6       100     -
chr2  133240474       133240574       7       100     +
chr9  131495427       131495527       8       100     +
chrX  125952943       125953043       9       100     +
chr3  59685545        59685645        10      100     +

Specify the number of intervals to generate.

The -n option allows one to override the default of generating 1 million intervals.

$ bedtools random -g hg19.genome -n 3
chr20 47975280        47975380        1       100     -
chr16 23381222        23381322        2       100     +
chr3  104913816       104913916       3       100     -

Specify the length of intervals to generate.

The -l option allows one to override the default interval length of 100bp.

$ bedtools random -g hg19.genome -l 5
chr9  54133731        54133736        1       5       +
chr1  235288830       235288835       2       5       -
chr8  26744718        26744723        3       5       +
chr3  187313616       187313621       4       5       -
chr11 88996846        88996851        5       5       -
chr13 84714855        84714860        6       5       -
chr13 10759738        10759743        7       5       -
chr6  122569739       122569744       8       5       +
chr17 50884025        50884030        9       5       -
chr11 38576901        38576906        10      5       +

Defining a seed for the random interval creation

bedtools random uses a pseudo-random number generator to permute the locations of BED features. Therefore, each run should produce a different result. This can be problematic if one wants to exactly recreate an experiment. By using the seed option, one can supply a custom integer seed for bedtools random. In turn, each execution of bedtools random with the same seed and input files should produce identical results.

$ bedtools random -g hg19.genome -seed 71346
chrY  23380696        23380796        1       100     -
chr14 94368315        94368415        2       100     +
chr14 45353323        45353423        3       100     -
chr14 100546766       100546866       4       100     -
chr12 43294368        43294468        5       100     -
chr1  141470585       141470685       6       100     -
chr10 31273665        31273765        7       100     +
chr5  19102979        19103079        8       100     +
chr3  116730634       116730734       9       100     -
chr3  101222965       101223065       10      100     -

# (same seed, thus same as above)
$ bedtools random -g hg19.genome -seed 71346
chrY  23380696        23380796        1       100     -
chr14 94368315        94368415        2       100     +
chr14 45353323        45353423        3       100     -
chr14 100546766       100546866       4       100     -
chr12 43294368        43294468        5       100     -
chr1  141470585       141470685       6       100     -
chr10 31273665        31273765        7       100     +
chr5  19102979        19103079        8       100     +
chr3  116730634       116730734       9       100     -
chr3  101222965       101223065       10      100     -

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