python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py M1.1-GSM3494248.end1.fastq.gz M1.1-GSM3494248.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/Macaca_mulatta-Mmul_10/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/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - M1.1-GSM3494248.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py M1.2-GSM3494249.end1.fastq.gz M1.2-GSM3494249.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/Macaca_mulatta-Mmul_10/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/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - M1.2-GSM3494249.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py M1.1-GSM3494248.end1.fastq.gz M1.1-GSM3494248.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/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - M1.1-GSM3494248.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py M1.2-GSM3494249.end1.fastq.gz M1.2-GSM3494249.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/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - M1.2-GSM3494249.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique