python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.end1.fastq.gz 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.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/hg38+dm6/bowtie-indexes/hg38+dm6 -p 20 -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/bowtie-indexes/hg38+dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.end1.fastq.gz 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.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/hg38+dm6/bowtie-indexes/hg38+dm6 -p 20 -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/bowtie-indexes/hg38+dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.end1.fastq.gz 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.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/hg38+dm6/bowtie-indexes/hg38+dm6 -p 20 -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/bowtie-indexes/hg38+dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.end1.fastq.gz 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.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/hg38+dm6/bowtie-indexes/hg38+dm6 -p 20 -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/bowtie-indexes/hg38+dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.end1.fastq.gz 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.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/hg38+dm6/bowtie-indexes/hg38+dm6 -p 20 -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/bowtie-indexes/hg38+dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.end1.fastq.gz 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.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/hg38+dm6/bowtie-indexes/hg38+dm6 -p 20 -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/bowtie-indexes/hg38+dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique