###########################################################################
#
# Configuration file for chirp-seq command line run
#
# Please give the Whole Path of a file, and do not include space in file names
#
# example as follows
#
###########################################################################

evenlane_filename = /Users/kunqu/labmembers/chu/test/terc_even_supert.fastq
oddlane_filename = /Users/kunqu/labmembers/chu/test/terc_odd_supert.fastq
inputlane_filename = /Users/kunqu/labmembers/chu/test/terc_input_supert.fastq
mailto  = kqu@stanford.edu

scripts_directory = /seq/chirpseq
chromosome_size_file = /seq/chromosome/hg18/hg18.sizes
raw_read_length = 36
band_width = 200

bowtie_bin         = /seq/bowtie-0.12.6/bowtie
bowtie_index     = /seq/bowtie-0.12.6/indexes/hg18
bowtie_threads  = 6
macs_bin           = /seq/macs/bin/macs14

wigToBigWig = /seq/ucsc/wigToBigWig
bigWigToBedGraph = /seq/ucsc/bigWigToBedGraph
bedGraphToBigWig = /seq/ucsc/bedGraphToBigWig

