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.. _random:
###############
*random*
###############
|
.. image:: ../images/tool-glyphs/random-glyph.png
:width: 600pt
|
`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.
.. seealso::
:doc:`../tools/shuffle`
:doc:`../tools/jaccard`
==========================================================================
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``.
.. code-block:: bash
$ 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.
.. code-block:: bash
$ 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.
.. code-block:: bash
$ 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.
.. code-block:: bash
$ 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 -
|
