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.
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. |
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 +
-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 -
-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 +
-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 -
