diff --git a/docs/content/tools/subtract.rst b/docs/content/tools/subtract.rst index 91282858e5a7caaba49964d870d70c32c2b6d423..5c05be3036abaf4885170534f41a38998d2ec8eb 100755 --- a/docs/content/tools/subtract.rst +++ b/docs/content/tools/subtract.rst @@ -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 + ========================================================================== diff --git a/docs/content/tools/window.rst b/docs/content/tools/window.rst index df7f6858bc733fe9d57ba1ba46462c888a5c2b2d..dfb2db80e57288d533afd2a77778c0c1a8b40216 100755 --- a/docs/content/tools/window.rst +++ b/docs/content/tools/window.rst @@ -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