python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py FrozKera-DMSO-0h-a_R1.fastq.gz FrozKera-DMSO-0h-a_R2.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/hg19/bowtie-indexes/chrM -p 8 -v 2 --k 2 -m 1 -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/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2017-07-17-FrozKera-DMSO-0h-a_R1.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py FrozKera-DMSO-0h-b_R1.fastq.gz FrozKera-DMSO-0h-b_R2.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/hg19/bowtie-indexes/chrM -p 8 -v 2 --k 2 -m 1 -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/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2017-07-17-FrozKera-DMSO-0h-b_R1.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py FrozKera-DMSO-24h-a_R1.fastq.gz FrozKera-DMSO-24h-a_R2.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/hg19/bowtie-indexes/chrM -p 8 -v 2 --k 2 -m 1 -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/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2017-07-17-FrozKera-DMSO-24h-a_R1.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py FrozKera-DMSO-24h-b_R1.fastq.gz FrozKera-DMSO-24h-b_R2.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/hg19/bowtie-indexes/chrM -p 8 -v 2 --k 2 -m 1 -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/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2017-07-17-FrozKera-DMSO-24h-b_R1.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py FrozKera-DMSO-24hI-a_R1.fastq.gz FrozKera-DMSO-24hI-a_R2.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/hg19/bowtie-indexes/chrM -p 8 -v 2 --k 2 -m 1 -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/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2017-07-17-FrozKera-DMSO-24hI-a_R1.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py FrozKera-DMSO-24hI-b_R1.fastq.gz FrozKera-DMSO-24hI-b_R2.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/hg19/bowtie-indexes/chrM -p 8 -v 2 --k 2 -m 1 -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/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2017-07-17-FrozKera-DMSO-24hI-b_R1.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py FrozKera-DMSO-6h-a_R1.fastq.gz FrozKera-DMSO-6h-a_R2.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/hg19/bowtie-indexes/chrM -p 8 -v 2 --k 2 -m 1 -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/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2017-07-17-FrozKera-DMSO-6h-a_R1.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py FrozKera-DMSO-6h-b_R1.fastq.gz FrozKera-DMSO-6h-b_R2.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/hg19/bowtie-indexes/chrM -p 8 -v 2 --k 2 -m 1 -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/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2017-07-17-FrozKera-DMSO-6h-b_R1.2x36mers.chrM