python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.end1.fastq.gz 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 - 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.end1.fastq.gz 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 - 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.end1.fastq.gz 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 - 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.end1.fastq.gz 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 - 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.end1.fastq.gz 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 - 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.end1.fastq.gz 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 - 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.end1.fastq.gz 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 - 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.end1.fastq.gz 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 - 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.end1.fastq.gz 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 - 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.end1.fastq.gz 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 - 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.end1.fastq.gz 2026-04-24-MS260403L04_exp260316_RPE1_t18h_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 - 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.end1.fastq.gz 2026-04-24-MS260403L05_exp260316_RPE1_t43h_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 - 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.end1.fastq.gz 2026-04-24-MS260403L06_exp260316_RPE1_t90h_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 - 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.end1.fastq.gz 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-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 - 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.end1.fastq.gz 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-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 - 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.end1.fastq.gz 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-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 - 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.end1.fastq.gz 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-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 - 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.end1.fastq.gz 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-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 - 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x36mers.hg38+dm6.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.end1.fastq.gz 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-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 - 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x36mers.hg38+dm6.unique