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bedtools ClosestBed (version 2.30.0)

BED/bedGraph/GFF/VCF/EncodePeak file:

Overlap with: will you select a BED/bedGraph/GFF/VCF/EncodePeak file from your history or use a built-in GFF file?:

Built-in GFF files contain full annotation of a reference genome

Select a BED/bedGraph/GFF/VCF/EncodePeak file:

How ties for closest feature should be handled:

This occurs when two features in B have exactly the same overlap with a feature in A.

Calculation based on strandedness?:

In addition to the closest feature in B, report its distance to A as an extra column:

The reported distance for overlapping features will be 0

Add additional columns to report distance to upstream feature. Distance defintion:

Like -d, report the closest feature in B, and its distance to A as an extra column. However unlike -d, use negative distances to report upstream features

Report the k closest hits:

Ignore features in B that overlap A:

That is, we want close, yet not touching features only

How multiple databases are resolved:

What it does

Similar to intersectBed, closestBed searches for overlapping features in A and B. In the event that no feature in B overlaps the current feature in A, closestBed will report the closest (that is, least genomic distance from the start or end of A) feature in B. For example, one might want to find which is the closest gene to a significant GWAS polymorphism. Note that closestBed will report an overlapping feature as the closest—that is, it does not restrict to closest non-overlapping feature.

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