ASAP_configFile_example.conf

#NOTE: General parameters section must be always filled no matter the preformed step. 
#BAM option: a bam file must be provided if one is interested only in one of the post-mapping steps. If this is the case, map option must be set to "no"
#NOTE: When running the pipeline, only the "turned on" section are considered (+ general parameters). A section is turned on by yes/no arguments. 


#===============================================================================
#============================== General parameters =============================
#===============================================================================

#Main output directory where results written. OUTDIR is created if does not exist. Defaut: current diretory
OUTDIR=.

#Directory where a temporary folder is created to hold temporary files. Default: current directory
TMPDIR=.

#Name of the processed sample (no space allowed. Use _/- to mimic space if needed). SampleName will be used in naming the output files.
sampleName=test

#chromsomes length (tab-delimited format: <Chr name><chr length>)
CHRLEN=docs/TAIR10_chrLen.txt


#path to dependencies
pathSamtools=/usr/local/bin/samtools
pathBowtie2=/usr/local/bin/bowtie2
pathMACS2=/usr/local/bin/macs2
pathGenomeCoverageBed=/usr/local/bin/genomeCoverageBed
pathToJava=/usr/bin/java
pathToPicardJar=/usr/local/src/picard-20150223/dist/picard.jar

#===============================================================================
#============================== Mapping step ===================================
#===============================================================================

#Perform mapping step? Possible values: yes/no
map=yes

#Path to fastq files (files can be gzipped)
FASTQ1=test_data/toy.fastq1.fq.gz
FASTQ2=test_data/toy.fastq2.fq.gz

#path to bowtie indexes
bowtieIndex=docs/TAIR10

#bowtie2 mapping paramters
mappingParameters="--very-sensitive -X 2000 -p 10"

#=========================== Post-mapping steps ================================

#Provide own BAM file if intrested only in the post-mapping steps (map option must be set to "no").
BAM=test_data/ASAPtest.bam


#===============================================================================
#============================= Filterings step =================================
#===============================================================================

#Perform the filtering step? possible values: yes/no
filter=yes

#Maximum number of mismatches allowed
maxMis=1

#Minimum mapping quality
mapQual=10

#Filter reads by blacklist of regions? possible values: yes/no
blacklist=yes

#blacklisted regions (reads falling into theses regions are removed). regions: <chr><start><end>
blacklistedRegions=docs/blacklisted_ATACseq_regions_tair10.bed

#Shift reads by 4bp so that read starts reflect the center of the Tn5 transposition event
shift=yes

#===============================================================================
#============================= Coverage step ===================================
#===============================================================================

#Compute read coverage? coverage of insertion events? possible values: yes/no
readCoverage=yes
ieventsCoverage=yes

#===============================================================================
#===================== Fragment length distribution ============================
#===============================================================================

##Compute fragment length distribution? possible values: yes/no
fragDist=yes


#===============================================================================
#========= Extract read pairs based on fragment length range ====================
#===============================================================================

#extract read pairs based on a range of fragment length? possible values: yes/no
extractReads=yes

#Compute arcs between selected fragment extremities? possible values: yes/no
arcs=yes

#lower boundery of the range: [lowBoundary,upBoundary]
lowBoundary=100

#upper boundery of the range: [lowBoundary,upBoundary]
upBoundary=250

#===============================================================================
#============================= Peak calling ====================================
#===============================================================================

#perfom peak calling?
callpeak=yes

#control file (ATAC peak calling can be performed without a control, however, one can provide a control such as ATAC on genomic DNA..). Possible values: path to input BAM file/no value
control=

#Treatement file is either created within the pipeline or provided in the previous BAM option. 

modelParameters="--nomodel --shift -50 --extsize 100"
MODE=broad
fdr=0.01

#effective genome size
gsize=10e7


 #=============================================================================#
 # See README.txt for a detailed description and complete list of outputs      #
 #=============================================================================#