FreeHiC_parameters

projDir="/path/to/FreeHiC/repository"
fastqFile="ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1215nnn/GSM1215593/suppl/GSM1215593_trimmedAndFiltered-TROPHOZOITES-XL-AGGG-L2" #"${projDir}/demoData/GSM1215593_trimmedAndFiltered-TROPHOZOITES-XL-AGGG-L2"
ref="${projDir}/data/PlasmoDB-9.0_Pfalciparum3D7_Genome.fasta"
refrag="${projDir}/data/MboI_resfrag_plasmodium.bed"
simuName="demoSimulation"
outDir="${projDir}/results"
summaryFile="${projDir}/summary/${simuName}_FreeHiC.summary"

bwa="/path/to/bwa"
samtools="/path/to/samtools"
bedtools="/path/to/bedtools"

train=1
simulate=1
postProcess=1
coreN=4
mismatchN=3
gapN=1
mismatchP=""
gapP=""
chimericP=""
simuN=2400000
readLen=40
resolution=10000
lowerBound=$((resolution*2))
refragU=500
ligateSite="GATCGATC"