python ~/code/PEFastqToTabDelimited.py K562-CRISPRi-15776-a_S16_R1_001.fastq.gz K562-CRISPRi-15776-a_S16_R2_001.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/hg19-female -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.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L225-K562-CRISPRi-15776-a.2x36mers.hg19-female.unique
python ~/code/PEFastqToTabDelimited.py K562-CRISPRi-15776-b_S17_R1_001.fastq.gz K562-CRISPRi-15776-b_S17_R2_001.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/hg19-female -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.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L226-K562-CRISPRi-15776-b.2x36mers.hg19-female.unique
python ~/code/PEFastqToTabDelimited.py K562-CRISPRi-15777-a_S18_R1_001.fastq.gz K562-CRISPRi-15777-a_S18_R2_001.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/hg19-female -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.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L227-K562-CRISPRi-15777-a.2x36mers.hg19-female.unique
python ~/code/PEFastqToTabDelimited.py K562-CRISPRi-15777-b_S19_R1_001.fastq.gz K562-CRISPRi-15777-b_S19_R2_001.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/hg19-female -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.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L228-K562-CRISPRi-15777-b.2x36mers.hg19-female.unique
python ~/code/PEFastqToTabDelimited.py K562-CRISPRi-N-b_S15_R1_001.fastq.gz K562-CRISPRi-N-b_S15_R2_001.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/hg19-female -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.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L224-K562-CRISPRi-N-b.2x36mers.hg19-female.unique
python ~/code/PEFastqToTabDelimited.py K562-CRISPRk-N-a_S20_R1_001.fastq.gz K562-CRISPRk-N-a_S20_R2_001.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/hg19-female -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.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L229-K562-CRISPRk-N-a.2x36mers.hg19-female.unique
python ~/code/PEFastqToTabDelimited.py K562-CRISPRk-N-b_S21_R1_001.fastq.gz K562-CRISPRk-N-b_S21_R2_001.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/hg19-female -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.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L230-K562-CRISPRk-N-b.2x36mers.hg19-female.unique