[data] 
# directories for bpmap and CEL files
# GenomeGrp: Genome Group name in bpmap file. Hs for Affy human Tiling 1.0 and 2.0 arrays
# ''(blank) for Affy old Chr21/22 and Encode arrays; Mouse: Mm; Drosophila: Dm.Celegans: Ce; S.pombe: Sp
# bpmap and cel files should be in the same order and have the same keys (item before =)
# RepLib: full name of the the Repeat library file (optional)
# Group: separates all your cel files into Treatment (1) or Control (0) groups (e.g. 111000 for 3ChIP and 3Input, 10 for 1ChIP 1Ipnut, etc)
# Paired: Specify 1 if the treatment and control experiments are strictly paired, otherwise leave it blank.
# If paired, the cel files should be well aligned, like: ChIP1 ChIP2 ChIP3 Ctrl1 Ctrl2 Ctrl3 

BpmapFolder = /misc/iris/acct/weili/database/BPmap/Chr2122
CelFolder = /misc/iris/acct/weili/Tiling.Soft/Model.Tiling/lab/ER
GenomeGrp =
RepLib = /misc/iris/acct/weili/database/humanhg17_May2004/Annotation/Humanhg17Rep.lib
Group = 111000
Pair = 

[bpmap]
1 = P1_CHIP_A.Anti-Sense.hs.NCBIv35.NR.bpmap
2 = P1_CHIP_B.Anti-Sense.hs.NCBIv35.NR.bpmap
3 = P1_CHIP_C.Anti-Sense.hs.NCBIv35.NR.bpmap

[cel]
1 = MCF_ER_A1.CEL  MCF_ER_A3.CEL  MCF_ER_A4.CEL MCF_INP_A1.CEL  MCF_INP_A3.CEL  MCF_INP_A4.CEL
2 = MCF_ER_B1.CEL  MCF_ER_B3.CEL  MCF_ER_B4.CEL MCF_INP_B1.CEL  MCF_INP_B3.CEL  MCF_INP_B4.CEL
3 = MCF_ER_C1.CEL  MCF_ER_C3.CEL  MCF_ER_C4.CEL MCF_INP_C1.CEL  MCF_INP_C3.CEL  MCF_INP_C4.CEL

[intensity analysis]
# BandWidth: 	the number of bases to extended from the position being analyzed. 
# The result is that 2*Bandwidth probe positions are included in the signal and p-value analysis
# MaxGap: 	maximum gap between positive probes; All regions separated by < MaxGap will be mergered into one 
# MinProbe: 	minimum number of probes for MATCh score analysis 
# Var:          control the variance from the input (usually you need at least 3 input replicates to turn on this option)

BandWidth = 	300
MaxGap = 	300
MinProbe  = 	10	
Var = 0

[interval analysis]
# interval cutoff can be from either MAT score or pvalue or qvalue(FDR)  
# if multiple cutoffs are specified, only one will be used as the real cutoff, others will be ignored.
# cutoff priority: Qvalue > Pvalue > Matscore 
# default is Pvalue 1e-5
# Extend: extend the ChIP-enriched regions at both ends, default is 0.
# set it a negative number if you want to shrink the regions.

Matscore = 
Pvalue = 1e-5
FDR = 
Extend = 

[output]
# Log: the screen output will be stored in a file if it is 1 or stderr if it is ''(blank)

Log =