5.13 shuffleBed¶
shuffleBed will randomly permute the genomic locations of a fearure file among a genome defined in a genome file. One can also provide an “exclusions” BED/GFF/VCF file that lists regions where you do not want the permuted features to be placed. For example, one might want to prevent features from being placed in known genome gaps. shuffleBed is useful as a null basis against which to test the significance of associations of one feature with another.
5.13.1 Usage and option summary¶
Usage:
shuffleBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME>
| Option | Description |
|---|---|
| -excl | A BED file of coordinates in which features from -i should not be placed (e.g., genome gaps). |
| -chrom | Keep features in -i on the same chromosome. Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. |
| -seed | Supply an integer seed for the shuffling. This will allow feature shuffling experiments to be recreated exactly as the seed for the pseudo-random number generation will be constant. By default, the seed is chosen automatically. |
5.13.2 Default behavior¶
By default, shuffleBed will reposition each feature in the input BED file on a random chromosome at a random position. The size and strand of each feature are preserved.
For example:
cat A.bed
chr1 0 100 a1 1 +
chr1 0 1000 a2 2 -
cat my.genome
chr1 10000
chr2 8000
chr3 5000
chr4 2000
shuffleBed -i A.bed -g my.genome
chr4 1498 1598 a1 1 +
chr3 2156 3156 a2 2 -
5.13.3 (-chrom)Requiring that features be shuffled on the same chromosome¶
The “-chrom” option behaves the same as the default behavior except that features are randomly placed on the same chromosome as defined in the BED file.
For example:
cat A.bed
chr1 0 100 a1 1 +
chr1 0 1000 a2 2 -
cat my.genome
chr1 10000
chr2 8000
chr3 5000
chr4 2000
shuffleBed -i A.bed -g my.genome -chrom
chr1 9560 9660 a1 1 +
chr1 7258 8258 a2 2 -
5.13.4 Excluding certain genome regions from shuffleBed¶
One may want to prevent BED features from being placed in certain regions of the genome. For example, one may want to exclude genome gaps from permutation experiment. The “-excl” option defines a BED file of regions that should be excluded. shuffleBed will attempt to permute the locations of all features while adhering to the exclusion rules. However it will stop looking for an appropriate location if it cannot find a valid spot for a feature after 1,000,000 tries.
For example (note that the exclude file excludes all but 100 base pairs of the chromosome):
cat A.bed
chr1 0 100 a1 1 +
chr1 0 1000 a2 2 -
cat my.genome
chr1 10000
cat exclude.bed
chr1 100 10000
shuffleBed -i A.bed -g my.genome -excl exclude.bed
chr1 0 100 a1 1 +
Error, line 2: tried 1000000 potential loci for entry, but could not avoid excluded
regions. Ignoring entry and moving on.
For example (now the exclusion file only excludes the first 100 bases of the chromosome):
cat A.bed
chr1 0 100 a1 1 +
chr1 0 1000 a2 2 -
cat my.genome
chr1 10000
cat exclude.bed
chr1 0 100
shuffleBed -i A.bed -g my.genome -excl exclude.bed
chr1 147 247 a1 1 +
chr1 2441 3441 a2 2 -
5.13.5 Defining a “seed” for the random replacement.¶
shuffleBed uses a pseudo-random number generator to permute the locations of BED features. Therefore, each run should produce a different result. This can be problematic if one wants to exactly recreate an experiment. By using the “-seed” option, one can supply a custom integer seed for shuffleBed. In turn, each execution of shuffleBed with the same seed and input files should produce identical results.
For example (note that the exclude file below excludes all but 100 base pairs of the chromosome):
cat A.bed
chr1 0 100 a1 1 +
chr1 0 1000 a2 2 -
cat my.genome
chr1 10000
shuffleBed -i A.bed -g my.genome -seed 927442958
chr1 6177 6277 a1 1 +
chr1 8119 9119 a2 2 -
shuffleBed -i A.bed -g my.genome -seed 927442958
chr1 6177 6277 a1 1 +
chr1 8119 9119 a2 2 -
. . .
shuffleBed -i A.bed -g my.genome -seed 927442958
chr1 6177 6277 a1 1 +
chr1 8119 9119 a2 2 -
