############### 5.5 windowBed ############### Similar to **intersectBed**, **windowBed** searches for overlapping features in A and B. However, **windowBed** adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are "near" features in A to be detected. ========================================================================== 5.5.1 Usage and option summary ========================================================================== **Usage:** :: windowBed [OPTIONS] -a -b =========================== ========================================================================================================================================================= Option Description =========================== ========================================================================================================================================================= **-abam** BAM file A. Each BAM alignment in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe: For example: samtools view -b | windowBed -abam stdin -b genes.bed **-ubam** Write uncompressed BAM output. The default is write compressed BAM output. **-bed** When using BAM input (-abam), write output as BED. The default is to write output in BAM when using -abam. For example: windowBed -abam reads.bam -b genes.bed -bed **-w** Base pairs added upstream and downstream of each entry in A when searching for overlaps in B. *Default is 1000 bp*. **-l** Base pairs added upstream (left of) of each entry in A when searching for overlaps in B. *Allows one to create assymetrical "windows". Default is 1000bp*. **-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*. **-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. =========================== ========================================================================================================================================================= ========================================================================== 5.5.2 Default behavior ========================================================================== By default, **windowBed** adds 1000 bp upstream and downstream of each A feature and searches for features in B that overlap this "window". If an overlap is found in B, both the *original* A feature and the *original* B feature are reported. For example, in the figure below, feature B1 would be found, but B2 would not. :: Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "window" = 10 BED File A <----------*************----------> BED File B ^^^^^^^^ ^^^^^^ Result ======== For example: :: cat A.bed chr1 100 200 cat B.bed chr1 500 1000 chr1 1300 2000 windowBed -a A.bed -b B.bed chr1 100 200 chr1 500 1000 ========================================================================== 5.5.3 (-w)Defining a custom window size ========================================================================== Instead of using the default window size of 1000bp, one can define a custom, *symmetric* window around each feature in A using the **-w** option. One should specify the window size in base pairs. For example, a window of 5kb should be defined as **-w 5000**. For example (note that in contrast to the default behavior, the second B entry is reported): :: cat A.bed chr1 100 200 cat B.bed chr1 500 1000 chr1 1300 2000 windowBed -a A.bed -b B.bed -w 5000 chr1 100 200 chr1 500 1000 chr1 100 200 chr1 1300 2000 ========================================================================== 5.5.4 (-l and -r)Defining assymteric windows ========================================================================== One can also define asymmetric windows where a differing number of bases are added upstream and downstream of each feature using the **-l (upstream)** and **-r (downstream)** options. For example (note the difference between -l 200 and -l 300): :: cat A.bed chr1 1000 2000 cat B.bed chr1 500 800 chr1 10000 20000 windowBed -a A.bed -b B.bed -l 200 -r 20000 chr1 100 200 chr1 10000 20000 windowBed -a A.bed -b B.bed -l 300 -r 20000 chr1 100 200 chr1 500 800 chr1 100 200 chr1 10000 20000 ========================================================================== 5.5.5 (-sw)Defining assymteric windows based on strand ========================================================================== Especially when dealing with gene annotations or RNA-seq experiments, you may want to define asymmetric windows based on "strand". For example, you may want to screen for overlaps that occur within 5000 bp upstream of a gene (e.g. a promoter region) while screening only 1000 bp downstream of the gene. By enabling the **-sw** ("stranded" windows) option, the windows are added upstream or downstream according to strand. For example, imagine one specifies **-l 5000 -r 1000** as well as the **- sw** option. In this case, forward stranded ("+") features will screen 5000 bp to the *left* (that is, *lower* genomic coordinates) and 1000 bp to the *right* (that is, *higher* genomic coordinates). By contrast, reverse stranded ("-") features will screen 5000 bp to the *right* (that is, *higher* genomic coordinates) and 1000 bp to the *left* (that is, *lower* genomic coordinates). For example (note the difference between -l 200 and -l 300): :: cat A.bed chr1 10000 20000 A.forward 1 + chr1 10000 20000 A.reverse 1 - cat B.bed chr1 1000 8000 B1 chr1 24000 32000 B2 windowBed -a A.bed -b B.bed -l 5000 -r 1000 -sw chr1 10000 20000 A.forward 1 + chr1 1000 8000 B1 chr1 10000 20000 A.reverse 1 - chr1 24000 32000 B2 ========================================================================== 5.5.6 (-sm)Enforcing "strandedness" ========================================================================== This option behaves the same as the -s option for intersectBed while scanning for overlaps within the "window" surrounding A. See the discussion in the intersectBed section for details. ========================================================================== 5.5.7 (-u)Reporting the presence of at least one overlapping feature ========================================================================== This option behaves the same as for intersectBed while scanning for overlaps within the "window" surrounding A. See the discussion in the intersectBed section for details. ========================================================================== 5.5.8 (-c)Reporting the number of overlapping features ========================================================================== This option behaves the same as for intersectBed while scanning for overlaps within the "window" surrounding A. See the discussion in the intersectBed section for details. ========================================================================== 5.5.9 (-v)Reporting the absence of any overlapping features ========================================================================== This option behaves the same as for intersectBed while scanning for overlaps within the "window" surrounding A. See the discussion in the intersectBed section for details.