############### 5.7 subtractBed ############### **subtractBed** searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported. ========================================================================== 5.7.1 Usage and option summary ========================================================================== Usage: :: subtractBed [OPTIONS] -a -b =========================== =============================================================================================================================================================================================================== Option Description =========================== =============================================================================================================================================================================================================== **-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp). **-s** Force strandedness. That is, find the closest feature in B overlaps A on the same strand. *By default, this is disabled*. =========================== =============================================================================================================================================================================================================== ========================================================================== 5.7.2 Default behavior ========================================================================== Figure: :: Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BED FILE A ************* ****** BED File B ^^^^^^^^ ^^^^^^^^^^^ Result ========= For example: :: cat A.bed chr1 100 200 chr1 10 20 cat B.bed chr1 0 30 chr1 180 300 subtractBed -a A.bed -b B.bed chr1 100 180 ========================================================================== 5.7.3 (-f)Requiring a minimal overlap fraction before subtracting ========================================================================== This option behaves the same as the -f option for intersectBed. In this case, subtractBed will only subtract an overlap with B if it covers at least the fraction of A defined by -f. If an overlap is found, but it does not meet the overlap fraction, the original A feature is reported without subtraction. For example: :: cat A.bed chr1 100 200 cat B.bed chr1 180 300 subtractBed -a A.bed -b B.bed -f 0.10 chr1 100 180 subtractBed -a A.bed -b B.bed -f 0.80 chr1 100 200 ========================================================================== 5.7.4 (-s)Enforcing "strandedness" ========================================================================== This option behaves the same as the -s option for intersectBed while scanning for features in B that should be subtracted from A. See the discussion in the intersectBed section for details.