diff --git a/USAGE_EXAMPLES b/USAGE_EXAMPLES index 58c48f12575df2e19623e7678bef807e98c60ab4..679f7cc3a1449999ec1806cdfa28b5e53d4c778b 100755 --- a/USAGE_EXAMPLES +++ b/USAGE_EXAMPLES @@ -42,6 +42,37 @@ Free for non-profit or academic use. Please contact me for commercial use. $ intersectBed -a genes.bed -b LINES.bed | intersectBed -a stdin -b SINEs.bed -v + peIntersectBed. Reports overlaps between features in a "paired-end" BEDPE file and a regular BED feature file. + + OVERLAPS WITH PAIRED-END "ENDS" + 1. Which paired-end reads overlap with a repeat on EITHER end? + $ peIntersectBed -a reads.bedpe -b repeatMasked.bed -type either + + 2. Which structural variations overlap with a repeat on BOTH ends? + $ peIntersectBed -a reads.bedpe -b repeatMasked.bed -type both + + 3. Which paired-end reads DO NOT overlap with a repeat on either end? + $ peIntersectBed -a reads.bedpe -b repeatMasked.bed -type NEITHER + + 4. Which structural variations overlap with a repeat on ONE and ONLY ONE end? + $ peIntersectBed -a reads.bedpe -b repeatMasked.bed -type xor + + OVERLAPS WITH THE "SPAN" OF THE PAIRED-END READ OR EVENT + 1. Which pair-end reads overlap span a gap based on the "inner-span"? + E.g. Pair =====....................===== + Gap 0000000000000000 + + $ peIntersectBed -a reads.bedpe -b gaps.bed -type inspan + + + 2. Which pair-end reads overlap span a gene based on the "inner-span"? + E.g. Pair =====....................===== + Gene 00000000000000000000000 + + $ peIntersectBed -a reads.bedpe -b genes.bed -type outspan + + + closestBed. Very similar to intersectBed, but finds the closest (not necessarily overlapping) feature in B to each feature in A. If multiple features in B overlap a feature in A, the one with the highest overlap with respect to A is reported. @@ -51,8 +82,8 @@ Free for non-profit or academic use. Please contact me for commercial use. Allows input from stdin in the same manner as intersectBed (see #7). - subtractBed. For each feature in A, it returns the fraction of that feature that is not overlapped by B. If a feature in A is entirely "spanned" by - any feature in B, it will not be reported. + subtractBed. For each feature in A, it returns the fraction of that feature that is not overlapped by B. If a feature in A is entirely + "spanned" by any feature in B, it will not be reported. 1. Remove introns from genes. $ subtractBed -a genes.bed -b introns.bed