## Config file for CLIP-seq pipeline

############
##  PATH  ##
############
SAMTOOLS_PATH=/bioinfo/local/build/Centos/samtools/samtools-1.3/bin
BEDTOOLS_PATH=/bioinfo/local/build/Centos/bedtools/bedtools-2.25.0/bin
R_PATH=/bioinfo/local/build/Centos/R/R-3.4.0/bin
PYTHON_PATH=/bioinfo/local/build/Centos/python/python-2.7.12/bin
AWK_PATH=/usr/bin
CUTADAPT_PATH=/bioinfo/local/build/Centos/python/python-2.7.12/bin
TOPHAT_PATH=/bioinfo/users/mcadix/miniconda3/envs/python27/bin
JAVA_PATH=/bioinfo/local/build/Centos/java/jdk1.7.0_45/bin
PICARD_TOOLS=/bioinfo/local/build/Centos/picard/1.97
PIRANHA_PATH=/bioinfo/local/build/piranha/piranha-1.2.1/bin

###########
##  DIR  ##
###########
SCRIPTS=/bioinfo/users/mcadix/myGitLab/clip-seq/scripts
ANNOTATION_DIR=/bioinfo/users/mcadix/myGitLab/clip-seq/annotation


##################
##  ANNOTATION  ##
##################
BUILD_ANNOT=0
ORG=hg19
UCSC_EXPORT=refseq_export_hg19.csv
WINDOW_SIZE=500


################
##  TRIMMING  ##
################
ADAPTER5="GTTCAGAGTTCTACAGTCCGACGATC"
ADAPTER3="TGGAATTCTCGGGTGCCAAGG"
MIN_LENGTH_READS=19


###############
##  MAPPING  ##
###############
BOWTIE_INDEX=/data/annotations/Human/hg19/bowtie2_indexes/base/hg19
MAX_MULTIHITS=1
READ_MISMATCHES=2
GTF_FILE=/data/annotations/Human/hg19/hg19refGene.gtf
TRANSCRIPTOME_MAX_HITS=1


###############################
##  REMOVE DUPLICATED READS  ##
###############################
REMOVE_DUPLICATES=1


######################
##  PEAK DETECTION  ##
######################
MIN_MAPQ=20
BIN_SIZE=50
BACKGROUND_THRESHOLD=0.95


#############################
##  DIFFERENTIAL ANALYSIS  ##
#############################
COMBINE_SAMPLE=2,4,1,3
MIN_COUNT_PER_COND=10


