python ~/code/PEFastqToTabDelimited.py Light-L1-GSM2474306/SRR5222788_1.fastq.gz Light-L1-GSM2474306/SRR5222788_2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - Light-L1-GSM2474306/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py Light-L2-GSM2474307/SRR5222789_1.fastq.gz Light-L2-GSM2474307/SRR5222789_2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - Light-L2-GSM2474307/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py Light-H1-GSM2474308/SRR5222790_1.fastq.gz Light-H1-GSM2474308/SRR5222790_2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - Light-H1-GSM2474308/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py Light-H2-GSM2474309/SRR5222791_1.fastq.gz Light-H2-GSM2474309/SRR5222791_2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - Light-H2-GSM2474309/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py Dark-L1-GSM2474310/SRR5222792_1.fastq.gz Dark-L1-GSM2474310/SRR5222792_2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - Dark-L1-GSM2474310/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py Dark-L2-GSM2474311/SRR5222793_1.fastq.gz Dark-L2-GSM2474311/SRR5222793_2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - Dark-L2-GSM2474311/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py Dark-H1-GSM2474312/SRR5222794_1.fastq.gz Dark-H1-GSM2474312/SRR5222794_2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - Dark-H1-GSM2474312/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py Dark-H2-GSM2474313/SRR5222795_1.fastq.gz Dark-H2-GSM2474313/SRR5222795_2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - Dark-H2-GSM2474313/all.2x36mers.unique