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bedtools MapBed (version 2.30.0.3)

File A (BAM/BED/bedGraph/GFF/VCF/EncodePeak):

File B (BAM/BED/bedGraph/GFF/VCF/EncodePeak):

Minimum overlap required as a fraction of A:

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

Minimum overlap required as a fraction of B:

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

Require reciprocal overlap:

If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval

Calculation based on strandedness?:

Applying operations to columns from merged intervals

Applying operations to columns from merged intervals 0

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.

Print the header from the A file prior to results:

Genome file:

What it does

bedtools map allows one to map overlapping features in a B file onto features in an A file and apply statistics and/or summary operations on those features.

bedtools map requires each input file to be sorted by genome coordinate. For BED files, this can be done with sort -k1,1 -k2,2n. Other sorting criteria are allowed if a genome file (-g) is provides that specifies the expected chromosome order.

The map tool is substantially faster in versions 2.19.0 and later. The plot below demonstrates the increased speed when, for example, counting the number of exome alignments that align to each exon. The bedtools times are compared to the bedops bedmap utility as a point of reference.

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