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bedtools AnnotateBed (version 2.30.0)

BED/bedGraph/GFF/VCF/EncodePeak file:

Specify names for each file:

BED/bedGraph/GFF/VCF/EncodePeak files:

Calculation based on strandedness?:

Report the count of features followed by the % coverage for each annotation file:

Default is to report solely the fraction of -i covered by each file

Report the count of features followed by the % coverage for each annotation file:

Default is to report solely the fraction of the input file covered by each file

What it does

bedtools annotate, well, annotates one BED/bedGraph/GFF/VCF/EncodePeak file with the coverage and number of overlaps observed from multiple other BED/bedGraph/GFF/VCF/EncodePeak files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command.

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