python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_PBS_rep1-GSM7114217.end1.fastq.gz Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_PBS_rep1-GSM7114217.end2.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/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_PBS_rep1-GSM7114217.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-Vector_rep1-GSM7114219.end1.fastq.gz Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-Vector_rep1-GSM7114219.end2.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/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-Vector_rep1-GSM7114219.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_PBS_rep1-GSM7114217.end1.fastq.gz Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_PBS_rep1-GSM7114217.end2.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/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_PBS_rep1-GSM7114217.2x36mers.Mesocricetus_auratus-MesAur1.0_HiC+chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-Vector_rep1-GSM7114219.end1.fastq.gz Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-Vector_rep1-GSM7114219.end2.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/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-Vector_rep1-GSM7114219.2x36mers.Mesocricetus_auratus-MesAur1.0_HiC+chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-RBD_rep2-GSM7114222.end1.fastq.gz Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-RBD_rep2-GSM7114222.end2.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/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-RBD_rep2-GSM7114222.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-RBD_rep1-GSM7114221.end1.fastq.gz Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-RBD_rep1-GSM7114221.end2.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/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-RBD_rep1-GSM7114221.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-Vector_rep2-GSM7114220.end1.fastq.gz Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-Vector_rep2-GSM7114220.end2.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/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-Vector_rep2-GSM7114220.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_PBS_rep2-GSM7114218.end1.fastq.gz Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_PBS_rep2-GSM7114218.end2.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/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_PBS_rep2-GSM7114218.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-RBD_rep2-GSM7114222.end1.fastq.gz Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-RBD_rep2-GSM7114222.end2.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/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-RBD_rep2-GSM7114222.2x36mers.Mesocricetus_auratus-MesAur1.0_HiC+chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-RBD_rep1-GSM7114221.end1.fastq.gz Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-RBD_rep1-GSM7114221.end2.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/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-RBD_rep1-GSM7114221.2x36mers.Mesocricetus_auratus-MesAur1.0_HiC+chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-Vector_rep2-GSM7114220.end1.fastq.gz Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-Vector_rep2-GSM7114220.end2.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/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_dNS1-Vector_rep2-GSM7114220.2x36mers.Mesocricetus_auratus-MesAur1.0_HiC+chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_PBS_rep2-GSM7114218.end1.fastq.gz Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_PBS_rep2-GSM7114218.end2.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/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mesocricetus_auratus-MesAur1.0_HiC-DNAZoo/bowtie-indexes/Mesocricetus_auratus-MesAur1.0_HiC+chrM.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Golden_Hamster_Alveolar_Macrophage_2_weeks_post_vaccinated_with_PBS_rep2-GSM7114218.2x36mers.Mesocricetus_auratus-MesAur1.0_HiC+chrM.unique