Commit e5e5d751 authored by arq5x's avatar arq5x
Browse files

[DOC] fix docs typos

parent fe6b3098
......@@ -109,7 +109,7 @@ while scanning for features in B that should be subtracted from A.
chr1 180 300 b2 1 -
$ bedtools subtract -a A.bed -b B.bed -s
chr1 120 120 a1 1 +
chr1 120 200 a1 1 +
==========================================================================
......
......@@ -40,7 +40,7 @@ Option Description
**-r** Base pairs added downstream (right of) of each entry in A when searching for overlaps in B. *Allows one to create assymetrical "windows". Default is 1000bp*.
**-sw** Define -l and -r based on strand. For example if used, -l 500 for a negative-stranded feature will add 500 bp downstream. *By default, this is disabled*.
**-sm** Only report hits in B that overlap A on the same strand. *By default, overlaps are reported without respect to strand*.
**-Sm** Only report hits in B that overlap A on the same strand. *By default, overlaps are reported without respect to strand*.
**-Sm** Only report hits in B that overlap A on the opposite strand. *By default, overlaps are reported without respect to strand*.
**-u** Write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B.
**-c** For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B.
**-v** Only report those entries in A that have *no overlaps* with B.
......@@ -170,7 +170,7 @@ in B will only be included if the B interval is on the *same* strand as the A
interval.
==========================================================================
``-Sm`` Enforcing matches with the *same* "strandedness"
``-Sm`` Enforcing matches with the *opposite* "strandedness"
==========================================================================
This option behaves the same as the ``-S`` option for ``bedtools intersect`` while
scanning for overlaps within the "window" surrounding A. That is, overlaps in
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