FreeHiC_parameters_docker

## user defined input data file name
fastqFileName="GSM1215593_trimmedAndFiltered-TROPHOZOITES-XL-AGGG-L2"
refName="PlasmoDB-9.0_Pfalciparum3D7_Genome.fasta"
refragName="MboI_resfrag_plasmodium.bed"

## user defined simulation setting
simuName="demoSimulation"
train=0
simulate=1
postProcess=1
coreN=1
mismatchN=3
gapN=1
mismatchP=""
gapP=""
chimericP=""
simuN=2400
readLen=40
resolution=10000
lowerBound=$((resolution*2))
refragU=500
ligateSite="GATCGATC"

## user do not change! (Except for fastqFile variable if it is for the demo runs.)
projDir="/FreeHiC/"
outDir="/FreeHiC/results"
summaryFile="/FreeHiC/results/summary/${simuName}_FreeHiC.summary"

fastqFile="/FreeHiC/data/${fastqFileName}" ##For demo runs please use "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1215nnn/GSM1215593/suppl/GSM1215593_trimmedAndFiltered-TROPHOZOITES-XL-AGGG-L2"
ref="/FreeHiC/data/${refName}"
refrag="/FreeHiC/data/${refragName}"

bwa="bwa"
samtools="samtools"
bedtools="bedtools"