## Config file for 3-SMART pipeline


#############
##  PATHS  ##
#############

CUTADAPT_PATH=/bioinfo/local/build/Centos/python/python-2.7.12/bin
BOWTIE2_PATH=/bioinfo/local/build/Centos/bowtie2/bowtie2-2.2.5
SAMTOOLS_PATH=/bioinfo/local/build/Centos/samtools/samtools-1.1/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
JAVA_PATH=/bioinfo/local/build/Centos/java/jdk1.7.0_45/bin
#PICARD_TOOLS=/bioinfo/local/build/Centos/picard/1.97
FASTQC_PATH=/bioinfo/local/build/Centos/FastQC/FastQC_v0.11.5



## Please change the variable settings below if necessary

###########
##  DIR  ##
###########

SCRIPTS=/bioinfo/users/mcadix/myGitLab/3-smart/scripts
ANNOT_DIR=/bioinfo/users/mcadix/myGitLab/3-smart/annotation


################
##  TRIMMING  ##
################

RD_1_SP="ACACTCTTTCCCTACACG"
INDEX_SP="TCTGAACTCCAGTCAC"
MIN_LENGTH_READS=19


###############
##  MAPPING  ##
###############

RANDOM_HIT=1
SEED_LENGTH=22
MAX_MISMATCH_SEED=1
MIN_MAPQ=20
BOWTIE2_INDEX=/data/annotations/Human/hg19/bowtie2_indexes/base/hg19


###############################
##  REMOVE DUPLICATED READS  ##
###############################

#REMOVE_DUPLICATES=0


##################
##  ANNOTATION  ##
##################

BUILD_ANNOT=0
ORG=hg19
UCSC_EXPORT=refseq_export_hg19.csv
POLYA_MOTIF=./annotation/polyA_signal.csv


######################
##  PEAK DETECTION  ##
######################

MIN_MAPQ=20
MAX_DIST_MERGE=50
MIN_NB_READS_PER_PEAK=5


######################
##  PEAK FILTERING  ##
######################

LEXOGEN=0
NB_STRETCH_POLYA=9
MISM=1
NB_STRETCH_CONSECUTIVE=6
WINSIZE_DOWN=150
WINSIZE_UP=0
KEEP_LE_PEAKS=1
WINSIZE_DOWN_MOTIF=150
WINSIZE_UP_MOTIF=50

##################
##  ANNOTATION  ##
##################

MIN_LE_OV=1
MIN_INTRON_OV=3
MIN_ANNOT_OV=1


#########################
##  SAMPLE COMPARISON  ##
#########################

COMBINE_SAMPLE=2,4,1,3
MIN_COUNT_PER_COND=15
