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bedtools WindowBed (version 2.30.0)

BED/bedGraph/GFF/VCF/EncodePeak/BAM file:

BED/bedGraph/GFF/VCF/EncodePeak file:

When using BAM input, write output as BED. The default is to write output in BAM when using a BAM file:

Choose what you want to do:

Base pairs to add upstream and downstream:

Calculation based on strandedness?:

Write original A entry once if any overlaps found in B:

In other words, just report the fact at least one overlap was found in B

For each entry in A, report the number of hits in B:

Reports 0 for A entries that have no overlap with B

Only report those entries in A that have no overlaps with B:

Print the header from the A file prior to results:

What it does

Similar to bedtools intersect, window searches for overlapping features in A and B. However, window adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected.

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