python ~/code/PEFastqToTabDelimited.py PFL3-Apo-Rep1_S22_R1_001.fastq.gz PFL3-Apo-Rep1_S22_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L202-PFL3-Apo-Rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py PFL3-Apo-Rep2_S23_R1_001.fastq.gz PFL3-Apo-Rep2_S23_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L203-PFL3-Apo-Rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py PFL3-Apo-Rep3_S24_R1_001.fastq.gz PFL3-Apo-Rep3_S24_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L204-PFL3-Apo-Rep3.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py PFL3-Sym-Rep1_S25_R1_001.fastq.gz PFL3-Sym-Rep1_S25_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L205-PFL3-Sym-Rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py PFL3-Sym-Rep2_S26_R1_001.fastq.gz PFL3-Sym-Rep2_S26_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L206-PFL3-Sym-Rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py PFL3-Sym-Rep3_S27_R1_001.fastq.gz PFL3-Sym-Rep3_S27_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L207-PFL3-Sym-Rep3.2x36mers.unique