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diff --git a/docs/content/tools/slop.rst b/docs/content/tools/slop.rst
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--- a/docs/content/tools/slop.rst
+++ b/docs/content/tools/slop.rst
@@ -1,19 +1,39 @@
###############
*slop*
###############
-**slopBed** will increase the size of each feature in a feature file be a user-defined number of bases. While
-something like this could be done with an "**awk '{OFS="\t" print $1,$2-<slop>,$3+<slop>}'**",
-**slopBed** will restrict the resizing to the size of the chromosome (i.e. no start < 0 and no end >
-chromosome size).
+
+|
+
+.. image:: ../images/tool-glyphs/intersect-glyph.png
+ :width: 600pt
+
+|
+
+``bedtools slop`` will increase the size of each feature in a feature file be 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.
==========================================================================
Usage and option summary
==========================================================================
-Usage:
+**Usage**:
::
- slopBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
-
+
+ bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
+
+**(or):**
+
+ bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
+
=========================== ===============================================================================================================================================================================================================
Option Description
=========================== ===============================================================================================================================================================================================================
@@ -21,6 +41,8 @@ Usage:
**-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**
+**-header**
=========================== ===============================================================================================================================================================================================================
@@ -28,57 +50,92 @@ Usage:
==========================================================================
Default behavior
==========================================================================
-By default, **slopBed** will either add a fixed number of bases in each direction (**-b**) or an asymmetric
-number of bases in each direction (**-l** and **-r**).
+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``.
-For example:
-::
- cat A.bed
+
+.. code-block:: bash
+
+ $ cat A.bed
chr1 5 100
chr1 800 980
- cat my.genome
+ $ cat my.genome
chr1 1000
- slopBed -i A.bed -g my.genome -b 5
+ $ bedtools slop -i A.bed -g my.genome -b 5
chr1 0 105
chr1 795 985
- slopBed -i A.bed -g my.genome -l 2 -r 3
+ $ 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, **slopBed** will
-"clip" the feature accordingly.
-::
- cat A.bed
+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
+ $ cat my.genome
chr1 1000
- slopBed -i A.bed -g my.genome -b 5000
+ $ bedtools slop -i A.bed -g my.genome -b 5000
chr1 0 1000
chr1 0 1000
==========================================================================
-Resizing features according to strand
+``-s`` Resizing features according to strand
==========================================================================
-**slopBed** will optionally increase the size of a feature based on strand.
+**bedtools slop** will optionally increase the size of a feature based on strand.
For example:
-::
- cat A.bed
+
+.. code-block:: bash
+
+ $ cat A.bed
chr1 100 200 a1 1 +
chr1 100 200 a2 2 -
- cat my.genome
+ $ cat my.genome
chr1 1000
- slopBed -i A.bed -g my.genome -l 50 -r 80 -s
+ $ 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.
+