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####   CONFIGURATION FILE for ChIP-Seq  ####
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# This is the default configuration file for ChipSeq v2.1 Workflow
# Created by the installer on Fri Dec 13 18:08:42 CST 2013

################
## references ##
################
BWA_REF=/home/mayo/chipseq/reducedReferences/chr17.fa
CEAS_REF=/home/mayo/chipseq/reducedReferences/hg19.refGene
UCSC_REF_FLAT=/home/mayo/chipseq/reducedReferences/ucsc_refflat_hg19_chr17.txt
GENOME_TABLE=/home/mayo/chipseq/reducedReferences/genome_table.human.hg19.sorted.txt
IGV_REFERENCE_GENOME=/home/mayo/chipseq/reducedReferences/hg19.genome
#IGV_REFERENCE_GENOME=/home/mayo/chipseq/reducedReferences/hg19_chr17.genome
ANNOTATION_DIR=/home/mayo/chipseq/reducedReferences/annotation/
GENE_TSS=Hg19.great2.0.genes.chr17.txt
ANTI_GAP=hg19.non_gap_chr17.bed
TEST_TERM=hs.GO_annotation.txt
ANNO_TYPE=GO


###########
## tools ##
###########
CHIPSEQ_DIR=/home/mayo/chipseq
PYTHON=/usr/bin/python
SICER=/home/mayo/chipseq/tools/sicer/SICER_V1.1/SICER/
BWA_PATH=/home/mayo/chipseq/tools/bwa/bwa-0.5.9rc1
MACS_PATH=/home/mayo/chipseq/tools/macs2/bin/
MACS_PYTHON=/home/mayo/chipseq/tools/macs2//lib/python2.7/site-packages
CEAS_PATH=/home/mayo/chipseq/tools/ceas/CEAS-Package-1.0.2/bin/
CEAS_PYTHON=/home/mayo/chipseq/tools/ceas/CEAS-Package-1.0.2/lib/python2.7/site-packages/
JAVA=/home/mayo/chipseq/tools/java/jdk1.7.0_45/bin/java
SAMTOOLS=/home/mayo/chipseq/tools/samtools/samtools-0.1.19/
BEDTOOLS=/home/mayo/chipseq/tools/bedtools/bedtools-2.17.0/bin
PICARD=/home/mayo/chipseq/tools/picard/picard-tools-1.97
FASTQC=/home/mayo/chipseq/tools/fastqc//FastQC/fastqc
R_PATH=/home/mayo/chipseq/tools/R/R-2.14.0/bin/R
MEME_PATH=/home/mayo/chipseq/tools/meme/bin/meme
WIG2BIGWIG=/home/mayo/chipseq/tools/wigtobigwig//wigToBigWig
IGVTOOLS=/home/mayo/chipseq/tools/igvtools/IGVTools/igvtools

###############
## Constants ##
###############
IGV_LINK=ftp://my_server/prefix
IGV_SETUP_PDF=/home/mayo/chipseq/reducedReferences/IGV_Setup.pdf
WORKFLOW_SUMMARY_DOC=/home/mayo/chipseq/reducedReferences/HiCHIP_workflow_summary.doc
WORKFLOW_SUMMARY_IMG=/home/mayo/chipseq/reducedReferences/chipseq-pic.jpg
TOOL_VERSION=ChipSeq.2.0
ORGANISM=human
LOCATION=MySite
PLATFORM=Illumina

#### [Samtools] track_color_list.txt, FRAGMENT_SIZE, and STEP_SIZE are used to generate raw bedgraph/wig files
TCLR_LIST=/home/mayo/chipseq/reducedReferences/track_color_list.txt
FRAGMENT_SIZE=200
STEP_SIZE=20

#### parameters for BWA mapping
## if single end reads (SE), please specify "MAP_SE_ARGS" and "MAP_BOTH_ARGS"
## if paired-end reads (PE), please specify "MAP_PE_ARGS" and "MAP_BOTH_ARGS"
MAP_SE_ARGS=-n 10
MAP_PE_ARGS=-n 10 -a 500 -o 10000 -N 10 -s
MAP_BOTH_ARGS=-o 1 -l 32 -t 4 -k 2 -m 80000000

#### process mapped reads
## "MAPPING_QUALITY" is the cutoff for filtering out low mapping quality reads, only for SE data
## If you do not want to filter out low mapping quality reads, specify as "0", [default: 0] 
## Specify "dedup" if you want to remove duplicates, otherwise specify "nodedup", [default: dedup] 
MAP_QUALITY=0

#### modifications:
## for "REMOVE_DUP", specify as "REMOVE_DUP=dedup" (remove duplicates) or as "REMOVE_DUP=nodedup" (do not remove replicates)
REMOVE_DUP=dedup

## SICER Constants
SICER_ARGS=hg19 1 200 300 0.75 600 1E-2

## MACS2 Constants
MACS2_ARGS=-f BAM -g hs --keep-dup all -q 0.01
#MACS2_ARGS=-f BAM -g hs -s 100 --keep-dup 1 -q 0.01

## IDR Constants
IDR_ARGS=0.3 F p.value hg19
IDR_CUTOFF=0.01

## SGE Queue Constants
QUEUE=7-days

OPEN_SOURCE=true
