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bedtools FisherBed (version 2.30.0+galaxy1)

BED/bedGraph/GFF/VCF/EncodePeak file:

Genome file:

Calculation based on strandedness?:

Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage.:

If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data.

Minimum overlap required as a fraction of A:

Default is 1E-9, i.e. 1bp.

Require that the fraction of overlap be reciprocal for A and B:

In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.

Merge overlapping intervals before looking at overlap:

What it does

Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files.

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