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bedtools WindowBed

find overlapping intervals within a window around an interval (Galaxy Version 2.29.0)

Tool Parameters

Please provide a value for this option.

BED/bedGraph/GFF/VCF/BAM file * required

No compatible datasets available

Parameter 'inputB': specify a dataset of the required format / build for parameter

BED/bedGraph/GFF/VCF file * required

No datasets with bed, bedgraph, gff or vcf elements available

(-b)

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

(-bed)

Choose what you want to do

Base pairs to add upstream and downstream *

(-w)

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 (-u)

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

Reports 0 for A entries that have no overlap with B (-c)

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

(-v)

Print the header from the A file prior to results

(-header)

Additional Options

Email notification

Send an email notification when the job completes.

Help

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

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