Galaxy |

bedtools ShuffleBed (version 2.30.0+galaxy1)

BED/bedGraph/GFF/VCF/EncodePeak file:

The file is in BEDPE format:

Genome file:

Keep features in the input file on the same chromosome:

Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen.

Choose Seed?:

Choose an additional BED file:

Choose chromosome first:

Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size.

Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl:

Don’t allow shuffled intervals to overlap:

Allow the original the length of the original records to extebd beyond the length of the chromosome:

What it does

bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file. One can also provide an “exclusions” BED/bedGraph/GFF/VCF/EncodePeak 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. shuffle is useful as a null basis against which to test the significance of associations of one feature with another.

This tool is part of the bedtools package from the Quinlan laboratory.

Citation

If you use this tool in Galaxy, please cite:

Bjoern A. Gruening (2014), Galaxy wrapper