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.. _slop:
###############
*slop*
###############
|
.. image:: ../images/tool-glyphs/slop-glyph.png
:width: 600pt
|
``bedtools slop`` will increase the size of each feature in a feature file by a
user-defined number of bases. While something like this could be done with an
``awk '{OFS="\t" print $1,$2-<slop>,$3+<slop>}'``,
``bedtools slop`` will restrict the resizing to the size of the chromosome
(i.e. no start < 0 and no end > chromosome size).
.. note::
In order to prevent the extension of intervals beyond chromosome boundaries,
``bedtools slop`` requires a *genome* file defining the length of each
chromosome or contig.
.. seealso::
:doc:`../tools/flank`
==========================================================================
Usage and option summary
==========================================================================
**Usage**:
::
bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
**(or):**
::
slopBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
=========================== ===============================================================================================================================================================================================================
Option Description
=========================== ===============================================================================================================================================================================================================
**-b** Increase the BED/GFF/VCF entry by the same number base pairs in each direction. *Integer*.
**-l** The number of base pairs to subtract from the start coordinate. *Integer*.
**-r** The number of base pairs to add to the end coordinate. *Integer*.
**-s** Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the *end* coordinate.
**-pct** Define -l and -r as a fraction of the feature's length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp "upstream". Default = false.
**-header** Print the header from the input file prior to results.
=========================== ===============================================================================================================================================================================================================
==========================================================================
Default behavior
==========================================================================
By default, ``bedtools slop`` will either add a fixed number of bases in each
direction (``-b``) or an asymmetric number of bases in each direction
with ``-l`` and ``-r``.
.. code-block:: bash
$ cat A.bed
chr1 5 100
chr1 800 980
$ cat my.genome
chr1 1000
$ bedtools slop -i A.bed -g my.genome -b 5
chr1 0 105
chr1 795 985
$ bedtools slop -i A.bed -g my.genome -l 2 -r 3
chr1 3 103
chr1 798 983
However, if the requested number of bases exceeds the boundaries of the
chromosome, ``bedtools slop`` will "clip" the feature accordingly.
.. code-block:: bash
$ cat A.bed
chr1 5 100
chr1 800 980
$ cat my.genome
chr1 1000
$ bedtools slop -i A.bed -g my.genome -b 5000
chr1 0 1000
chr1 0 1000
==========================================================================
``-s`` Resizing features according to strand
==========================================================================
``bedtools slop`` will optionally increase the size of a feature based on strand.
For example:
.. code-block:: bash
$ cat A.bed
chr1 100 200 a1 1 +
chr1 100 200 a2 2 -
$ cat my.genome
chr1 1000
$ bedtools slop -i A.bed -g my.genome -l 50 -r 80 -s
chr1 50 280 a1 1 +
chr1 20 250 a2 2 -
==========================================================================
``-pct`` Resizing features by a given fraction
==========================================================================
``bedtools slop`` will optionally increase the size of a feature by a
user-specific fraction.
For example:
.. code-block:: bash
$ cat A.bed
chr1 100 200 a1 1 +
$ bedtools slop -i A.bed -g my.genome -b 0.5 -pct
chr1 50 250 a1 1 +
$ bedtools slop -i a.bed -l 0.5 -r 0.0 -pct -g my.genome
chr1 50 200 a1 1 +
==========================================================================
``-header`` Print the header for the A file before reporting results.
==========================================================================
By default, if your A file has a header, it is ignored when reporting results.
This option will instead tell bedtools to first print the header for the
A file prior to reporting results.
|
