python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3782-K562_KLF1_old_RIPA.250421_NB551514_0284_AHW7FKBGYW.end1.fastq.gz L3782-K562_KLF1_old_RIPA.250421_NB551514_0284_AHW7FKBGYW.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/bowtie-indexes/hg38-male -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/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3782-K562_KLF1_old_RIPA.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3783-K562_KLF1_new_RIPA.250421_NB551514_0284_AHW7FKBGYW.end1.fastq.gz L3783-K562_KLF1_new_RIPA.250421_NB551514_0284_AHW7FKBGYW.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/bowtie-indexes/hg38-male -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/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3783-K562_KLF1_new_RIPA.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3784-K562_H3K27ac_old_RIPA.250421_NB551514_0284_AHW7FKBGYW.end1.fastq.gz L3784-K562_H3K27ac_old_RIPA.250421_NB551514_0284_AHW7FKBGYW.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/bowtie-indexes/hg38-male -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/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3784-K562_H3K27ac_old_RIPA.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3785-K562_CTCF_old_RIPA.250421_NB551514_0284_AHW7FKBGYW.end1.fastq.gz L3785-K562_CTCF_old_RIPA.250421_NB551514_0284_AHW7FKBGYW.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/bowtie-indexes/hg38-male -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/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3785-K562_CTCF_old_RIPA.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3786-K562_H3K27ac_new_RIPA.250421_NB551514_0284_AHW7FKBGYW.end1.fastq.gz L3786-K562_H3K27ac_new_RIPA.250421_NB551514_0284_AHW7FKBGYW.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/bowtie-indexes/hg38-male -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/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3786-K562_H3K27ac_new_RIPA.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3787-K562_CTCF_new_RIPA.250421_NB551514_0284_AHW7FKBGYW.end1.fastq.gz L3787-K562_CTCF_new_RIPA.250421_NB551514_0284_AHW7FKBGYW.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/bowtie-indexes/hg38-male -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/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3787-K562_CTCF_new_RIPA.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3788-K562_Input_old_RIPA.250421_NB551514_0284_AHW7FKBGYW.end1.fastq.gz L3788-K562_Input_old_RIPA.250421_NB551514_0284_AHW7FKBGYW.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/bowtie-indexes/hg38-male -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/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3788-K562_Input_old_RIPA.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3789-K562_Input_new_RIPA.250421_NB551514_0284_AHW7FKBGYW.end1.fastq.gz L3789-K562_Input_new_RIPA.250421_NB551514_0284_AHW7FKBGYW.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/bowtie-indexes/hg38-male -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/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3789-K562_Input_new_RIPA.2x36mers.unique