Map the peaks in <peaks file> to genes in <knownGene file>. <knownGene file> isformat is as specified in http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.sql.<peaks file> format is as produced by MACS. If *auto* is chosen (default) file extension is examined for *.xls* for default MACS format or *.bed* for BED format. If the --detail option is provided, the following extra fields are appended to each row:
peak loc, dist from feature, map type, map subtype
chipsequtil
map_to_known_genes.py
$tss
--peaks-format=$peaks_fmt
--upstream-window=$upst_win
--downstream-window=$dnst_win
--map-output="$peaksOutput"
$detail
$intergenic
$knownGeneFile $knownGeneRef $macsPeaksFile