python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.end1.fastq.gz 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 - 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.end1.fastq.gz 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 - 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.end1.fastq.gz 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 - 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.end1.fastq.gz 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 - 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.end1.fastq.gz 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 - 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.end1.fastq.gz 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 - 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.end1.fastq.gz 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 - 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.end1.fastq.gz 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 - 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.end1.fastq.gz 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 - 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.end1.fastq.gz 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 - 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.end1.fastq.gz 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 - 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.end1.fastq.gz 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 - 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique