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Map Peaks to Known Genes (version 0.1)

knownGene file:

knownGene xRef file:

Peaks File:

Upstream Window:

Window width in base pairs to consider promoter region [default: %default]

Downstream Window:

Window width in base pairs to consider downstream region [default: %default]

Calculate downstream window from transcription start site instead of transcription end site:

Peaks Format:

Format of peaks input file

Append the following fields to each row: peak loc, dist from feature, map type, map subtype:

Write intergenic peaks to the gene file as well with None as gene ID: