python /home/users/marinovg/code/PEFastqToTabDelimited.py L99-CC7_MF2.2b-2017_11_29-rep1-Input_old_protocol_new_kit.end1.36mers.fastq.gz L99-CC7_MF2.2b-2017_11_29-rep1-Input_old_protocol_new_kit.end2.36mers.fastq.gz | /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 - L99-CC7_MF2.2b-2017_11_29-rep1-Input_old_protocol_new_kit.2x36mers.Aiptasia_pallida-1.0.unique
python /home/users/marinovg/code/PEFastqToTabDelimited.py L100-CC7_MF2.2b-2017_11_29-rep1-Input_new_protocol_new_kit.end1.36mers.fastq.gz L100-CC7_MF2.2b-2017_11_29-rep1-Input_new_protocol_new_kit.end2.36mers.fastq.gz | /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 - L100-CC7_MF2.2b-2017_11_29-rep1-Input_new_protocol_new_kit.2x36mers.Aiptasia_pallida-1.0.unique
zcat L99-CC7_MF2.2b-2017_11_29-rep1-Input_old_protocol_new_kit.end1.36mers.fastq.gz | /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 --sam - | /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 - L99-CC7_MF2.2b-2017_11_29-rep1-Input_old_protocol_new_kit.1x36mers.Aiptasia_pallida-1.0.unique
zcat L100-CC7_MF2.2b-2017_11_29-rep1-Input_new_protocol_new_kit.end1.36mers.fastq.gz | /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 --sam - | /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 - L100-CC7_MF2.2b-2017_11_29-rep1-Input_new_protocol_new_kit.1x36mers.Aiptasia_pallida-1.0.unique