#STARlong_PATH="/sc/orga/projects/schzrnas/sjzhu/bitbucket/STAR/STAR/source/"
#STARshort_PATH="/sc/orga/projects/schzrnas/sjzhu/bitbucket/STARshort/STAR/source/"
#samtools_PATH="/hpc/packages/minerva-common/samtools/1.1/bin/"
#bedtools_PATH="/hpc/packages/minerva-common/BEDTools/2.27.1/bin/"
#kallisto_PATH="/hpc/packages/minerva-common/kallisto/0.45.0/kallisto_linux-v0.45.0/"
#export PATH=$PATH:$STARlong_PATH:$STARshort_PATH:$samtools_PATH:$bedtools_PATH:$kallisto_PATH
library(STAR2bSMRT,lib.loc="/hpc/users/xzhus01/schzrnas/sjzhu/Project/NRXN/code/STAR2bSMRT/forRelease/r2")
genomeDir="/sc/orga/projects/schzrnas/sjzhu/Project/NRXN/data/IDPtest_ErinData/starShort/genomeDir_1pass"
genomeFasta = "/hpc/users/xzhus01/schzrnas/sjzhu/RNAseq/Reference/hg19/reference/hg19.fa"
chrom = "chr2"
s = 50147488
e = 51259537
cores = 10
thresSR=c(1:100)
thresDis=c(0:30)
adjustNCjunc=TRUE
fixedMatchedLS=FALSE
useSJout=FALSE
fuzzyMatch=100
folder="/hpc/users/xzhus01/schzrnas/sjzhu/Project/NRXN/test/PackageReleaseResult2/"
system( paste("mkdir -p",folder) )
########################################################################################################################
########################################## Adult2: adult_dlPFC1_10 ##################################################
########################################################################################################################
LRphqv="/hpc/users/xzhus01/schzrnas/sjzhu/Project/NRXN/data/Cleaned_primerR2/26963/polished_high_qv_consensus_isoforms.fasta"
SR1="/hpc/users/xzhus01/schzrnas/sjzhu/Project/NRXN/data/Cleaned_targetShortRead/CG1709012_R1/14-34-adult-dIPFC_S2_R1_001.fastq.gz"
SR2="/hpc/users/xzhus01/schzrnas/sjzhu/Project/NRXN/data/Cleaned_targetShortRead/CG1709012_R1/14-34-adult-dIPFC_S2_R2_001.fastq.gz"
outputDir=paste0(folder,"Adult2_adult_dlPFC1_10")
STAR2bSMRT_NRXN( genomeDir=genomeDir, genomeFasta=genomeFasta, LRphqv=LRphqv, LRflnc=NULL, LRnfl=NULL,
SR1=SR1, SR2=SR2, useSJout=useSJout, adjustNCjunc=adjustNCjunc,
thresSR=thresSR, thresDis=thresDis, outputDir=outputDir,
fixedMatchedLS=fixedMatchedLS, fuzzyMatch=fuzzyMatch,
chrom=chrom , s=s , e=e , cores=cores )
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