############### 5.14 slopBed ############### **slopBed** will increase the size of each feature in a feature file be a user-defined number of bases. While something like this could be done with an "**awk '{OFS="\t" print $1,$2-,$3+}'**", **slopBed** will restrict the resizing to the size of the chromosome (i.e. no start < 0 and no end > chromosome size). ========================================================================== 5.14.1 Usage and option summary ========================================================================== Usage: :: slopBed [OPTIONS] -i -g [-b or (-l and -r)] =========================== =============================================================================================================================================================================================================== Option Description =========================== =============================================================================================================================================================================================================== **-b** Increase the BED/GFF/VCF entry by the same number base pairs in each direction. *Integer*. **-l** The number of base pairs to subtract from the start coordinate. *Integer*. **-r** The number of base pairs to add to the end coordinate. *Integer*. **-s** Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the *end* coordinate. =========================== =============================================================================================================================================================================================================== ========================================================================== 5.14.2 Default behavior ========================================================================== By default, **slopBed** will either add a fixed number of bases in each direction (**-b**) or an asymmetric number of bases in each direction (**-l** and **-r**). For example: :: cat A.bed chr1 5 100 chr1 800 980 cat my.genome chr1 1000 slopBed -i A.bed -g my.genome -b 5 chr1 0 105 chr1 795 985 slopBed -i A.bed -g my.genome -l 2 -r 3 chr1 3 103 chr1 798 983 However, if the requested number of bases exceeds the boundaries of the chromosome, **slopBed** will "clip" the feature accordingly. :: cat A.bed chr1 5 100 chr1 800 980 cat my.genome chr1 1000 slopBed -i A.bed -g my.genome -b 5000 chr1 0 1000 chr1 0 1000 ========================================================================== 5.14.3 Resizing features according to strand ========================================================================== **slopBed** will optionally increase the size of a feature based on strand. For example: :: cat A.bed chr1 100 200 a1 1 + chr1 100 200 a2 2 - cat my.genome chr1 1000 slopBed -i A.bed -g my.genome -l 50 -r 80 -s chr1 50 280 a1 1 + chr1 20 250 a2 2 -