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bedtools Intersect intervals (version 2.30.0+galaxy1)

File A to intersect with B:

BAM/BED/bedGraph/GFF/VCF/EncodePeak format

Combined or separate output files:

File B to intersect with A:

BAM/BED/bedGraph/GFF/VCF/EncodePeak format

Calculation based on strandedness?:

What should be written to the output file?:

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.

Required overlap:

Report only those alignments that **do not** overlap with file(s) B:

Write the original A entry _once_ if _any_ overlaps found in B.:

Just report the fact >=1 hit was found

For each entry in A, report the number of overlaps with B.:

Reports 0 for A entries that have no overlap with B

When using BAM input, write output as BED instead of BAM.:

For coordinate sorted input file the more efficient sweeping algorithm is enabled.:

Genome file:

Only applies when used with -sorted option.

Genome file:

Print the header from the A file prior to results:

What it does

By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “overlap” with one another. This is known as feature intersection. bedtools intersect allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. bedtools intersect works with both BED/bedGraph/GFF/VCF/EncodePeak and BAM files as input.

Note that each BAM alignment is treated individually. Therefore, if one end of a paired-end alignment overlaps an interval in the BED file, yet the other end does not, the output file will only include the overlapping end.

Note that a BAM alignment will be sent to the output file once even if it overlaps more than one interval in the BED file.

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