python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Macaque_BA23_M3-GSM5765184.end1.fastq.gz Macaque_BA23_M3-GSM5765184.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 - Macaque_BA23_M3-GSM5765184.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Macaque_BA23_M2-GSM5765183.end1.fastq.gz Macaque_BA23_M2-GSM5765183.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 - Macaque_BA23_M2-GSM5765183.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Macaque_BA23_M3-GSM5765184.end1.fastq.gz Macaque_BA23_M3-GSM5765184.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 - Macaque_BA23_M3-GSM5765184.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Macaque_BA23_M2-GSM5765183.end1.fastq.gz Macaque_BA23_M2-GSM5765183.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 - Macaque_BA23_M2-GSM5765183.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Macaque_BA23_M4-GSM5765185.end1.fastq.gz Macaque_BA23_M4-GSM5765185.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 - Macaque_BA23_M4-GSM5765185.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Macaque_BA23_M1-GSM5765182.end1.fastq.gz Macaque_BA23_M1-GSM5765182.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 - Macaque_BA23_M1-GSM5765182.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Macaque_BA23_M4-GSM5765185.end1.fastq.gz Macaque_BA23_M4-GSM5765185.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 - Macaque_BA23_M4-GSM5765185.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Macaque_BA23_M1-GSM5765182.end1.fastq.gz Macaque_BA23_M1-GSM5765182.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 - Macaque_BA23_M1-GSM5765182.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique