python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_BFF1.end1.fastq.gz ATAC-seq_BFF1.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/Bubalus_bubalis-NDDB_SH_1/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/Bubalus_bubalis-NDDB_SH_1/bowtie-indexes/Bubalus_bubalis-NDDB_SH_1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_BFF1.2x36mers.chrM        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_BFF2.end1.fastq.gz ATAC-seq_BFF2.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/Bubalus_bubalis-NDDB_SH_1/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/Bubalus_bubalis-NDDB_SH_1/bowtie-indexes/Bubalus_bubalis-NDDB_SH_1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_BFF2.2x36mers.chrM        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_BFF1.end1.fastq.gz ATAC-seq_BFF1.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/Bubalus_bubalis-NDDB_SH_1/bowtie-indexes/Bubalus_bubalis-NDDB_SH_1 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_049568.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bubalus_bubalis-NDDB_SH_1/bowtie-indexes/Bubalus_bubalis-NDDB_SH_1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_BFF1.2x36mers.Bubalus_bubalis-NDDB_SH_1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_BFF2.end1.fastq.gz ATAC-seq_BFF2.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/Bubalus_bubalis-NDDB_SH_1/bowtie-indexes/Bubalus_bubalis-NDDB_SH_1 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_049568.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bubalus_bubalis-NDDB_SH_1/bowtie-indexes/Bubalus_bubalis-NDDB_SH_1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_BFF2.2x36mers.Bubalus_bubalis-NDDB_SH_1.unique