python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq__limb_stg30_wt_opossum_Rep-2.end1.fastq.gz ATAC-seq__limb_stg30_wt_opossum_Rep-2.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/Monodelphis_domestica/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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq__limb_stg30_wt_opossum_Rep-2.2x36mers.chrM        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq__limb_stg30_wt_opossum_Rep-1.end1.fastq.gz ATAC-seq__limb_stg30_wt_opossum_Rep-1.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/Monodelphis_domestica/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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq__limb_stg30_wt_opossum_Rep-1.2x36mers.chrM        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq__limb_stg30_wt_opossum_Rep-2.end1.fastq.gz ATAC-seq__limb_stg30_wt_opossum_Rep-2.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/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73 -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/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq__limb_stg30_wt_opossum_Rep-2.2x36mers.Monodelphis_domestica.BROADO5.73.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq__limb_stg30_wt_opossum_Rep-1.end1.fastq.gz ATAC-seq__limb_stg30_wt_opossum_Rep-1.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/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73 -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/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq__limb_stg30_wt_opossum_Rep-1.2x36mers.Monodelphis_domestica.BROADO5.73.unique