python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.end1.fastq.gz 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.end1.fastq.gz 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.end1.fastq.gz 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.end1.fastq.gz 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.end1.fastq.gz 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.end1.fastq.gz 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.end1.fastq.gz 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.end1.fastq.gz 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.end1.fastq.gz 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.end1.fastq.gz 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.end1.fastq.gz 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.end1.fastq.gz 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.end1.fastq.gz 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.end1.fastq.gz 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.end1.fastq.gz 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.end1.fastq.gz 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.end1.fastq.gz 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.end1.fastq.gz 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.end2.fastq.gz -trim 75 75 | /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 -e 200 -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 - 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique