SAMPLES=( 

READ_LENGTH=XXXXX
MINIMUM_FRAGMENT_SIZE=XXXXX

ADAPTER_SEQUENCE_MATE1=XXXXX
ADAPTER_SEQUENCE_MATE2=XXXXX

NUM_THREADS_PER_SAMPLE=3

### HG19 ###
STAR_INDEX=/ddn/gs1/shared/fargod/reference_genomes/hg19/hg19gencode/indexSTAR_gencode.v27lift37.annotation
GENE_MODEL=/ddn/gs1/shared/fargod/reference_genomes/hg19/hg19gencode/gencode.v27lift37.annotation/gencode.v27lift37.annotation.gtf
CHROM_SIZES=/ddn/gs1/home/bennettb/references/ucsc/hg19.chromSizes

NORMALIZATION_FACTOR=10000000

for (( i=0; i<${#SAMPLES[@]}; i++ ))
do

mkdir -p out/${SAMPLES[$i]}

READS_MATE1=/ddn/gs1/home/bennettb/data/Archer/17_11_RNA-Seq/${SAMPLES[$i]}.1.fastq
READS_MATE2=/ddn/gs1/home/bennettb/data/Archer/17_11_RNA-Seq/${SAMPLES[$i]}.2.fastq

nohup sh RUN_ONE_SAMPLE.sh ${SAMPLES[$i]} $READS_MATE1 $READS_MATE2 $ADAPTER_SEQUENCE_MATE1 $ADAPTER_SEQUENCE_MATE2 $READ_LENGTH $MINIMUM_FRAGMENT_SIZE $NUM_THREADS_PER_SAMPLE $STAR_INDEX $GENE_MODEL $CHROM_SIZES $NORMALIZATION_FACTOR > out/${SAMPLES[$i]}.log 2>&1 &
sleep 2500

done