5.1.29. random

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# 5.1.29. random

bedtools random will generate a random set of intervals in BED6 format. One can specify both the number (`-n`) and the size (`-l`) of the intervals that should be generated.

See also

shuffle jaccard

## 5.1.29.1. Usage and option summary

Usage:

    bedtools random [OPTIONS] -g <GENOME>

(or):

    randomBed [OPTIONS] -g <GENOME>

Option | Description
--- | ---
-l | The length of the intervals to generate. `Default = 100`
-n | The number of intervals to generate. `Default = 1,000,000`
-seed | Supply an integer seed for the shuffling. This will allow feature shuffling experiments to be recreated exactly as the seed for the pseudo-random number generation will be constant. By default, the seed is chosen automatically.

## 5.1.29.2. Default behavior

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     +

## 5.1.29.3. `-n` 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     -

## 5.1.29.4. `-l` 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       +

## 5.1.29.5. `-seed` 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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