############################################ 
####   CONFIGURATION FILE for ChIP-Seq  ####
############################################
# 9/3/13 - Raymond Moore
# This is the configuration file for ChipSeq v2.1 Workflow

################
## references ##
################
BWA_REF=/data2/bsi/reference/sequence/mouse/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0.1/genome.fa
#CEAS_REF=/data2/bsi/reference/chipseq/ref_files/hg19.refGene
UCSC_REF_FLAT=/data2/bsi/reference/sequence/mouse/Mus_musculus/UCSC/mm10/Annotation/Genes/refFlat.txt
GENOME_TABLE=/data2/bsi/reference/chipseq/ref_files/genome_table.mm10.txt
IGV_REFERENCE_GENOME=/data2/bsi/reference/misc/mm10.genome
ANNOTATION_DIR=/data2/bsi/reference/chipseq/ref_files/annotation/mouse/
GENE_TSS=Mm10.great2.0.genes.v2.txt
ANTI_GAP=mm10.non_gap.bed
TEST_TERM=Mm.GO_annotation.txt

###########
## tools ##
###########
CHIPSEQ_DIR=/data2/bsi/RandD/m088378/chipseq_wf/
SICER=/projects/bsi/bictools/apps/chipseq/sicer/1.1/
BWA_PATH=/projects/bsi/bictools/apps/alignment/bwa/0.5.9/
MACS_PATH=/projects/bsi/bictools/apps/chipseq/macs/2.0.10/bin/
CEAS_PATH=/projects/bsi/bictools/apps/chipseq/ceas/1.0.2/CEAS/bin/
JAVA=/usr/java/latest/bin/java
SAMTOOLS=/projects/bsi/bictools/apps/alignment/samtools/samtools-0.1.12a/
BEDTOOLS=/projects/bsi/bictools/apps/misc/BEDTools/2.16.2/bin/
PICARD=/projects/bsi/bictools/apps/alignment/picard/latest/
FASTQC=/projects/bsi/bictools/apps/qc/FastQC/fastqc
R_PATH=/usr/local/biotools/r/R-2.14.0/bin/R
GREAT_PATH=/projects/bsi/bictools/apps/chipseq/great/2.0.2/
MEME_PATH=/projects/bsi/bictools/apps/chipseq/meme/4.8.1/scripts/meme
WIG2BIGWIG=/projects/bsi/bictools/apps/visualizers/jksrc/bin/x86_64/wigToBigWig
NGS_PORTAL_PATH=/projects/bsi/bictools/apps/misc/ngs_dashboard/2.0
IGVTOOLS=/projects/bsi/bictools/apps/visualizers/igvtools/2.2.2/igvtools

###############
## Constants ##
###############
IGV_LINK=ftp://rcfisinl1-212/delivery
IGV_SETUP_PDF=/data2/bsi/reference/chipseq/ref_files/IGV_Setup.pdf
WORKFLOW_SUMMARY_DOC=/data2/bsi/reference/chipseq/ref_files/ChIP-Seq_workflow_summary.doc
TOOL_VERSION=ChipSeq.2.0
ORGANISM=mouse
LOCATION=Mayo
PLATFORM=Illumina

#### [Samtools] track_color_list.txt, FRAGMENT_SIZE, and STEP_SIZE are used to generate raw bedgraph/wig files
TCLR_LIST=/data2/bsi/reference/chipseq/ref_files/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=mm10 1 200 300 0.75 600 1E-2

## MACS2 Constants
MACS2_ARGS=-f BAM -g mm --keep-dup all -q 0.01

## IDR Constants
IDR_ARGS=0.3 F p.value mm10
IDR_CUTOFF=0.01

## SGE Queue Constants
QUEUE=7-days
