python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L464-Diamide-0_min-rep1/Diamide-0_min-rep1_S21_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L464-Diamide-0_min-rep1/L464-Diamide-0_min-rep1.181008_NB551514_0042_AH2JJGBGX9.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L464-Diamide-0_min-rep1/L464-Diamide-0_min-rep1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L464-Diamide-0_min-rep1/Diamide-0_min-rep1_S21_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L464-Diamide-0_min-rep1/L464-Diamide-0_min-rep1.181008_NB551514_0042_AH2JJGBGX9.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L464-Diamide-0_min-rep1/L464-Diamide-0_min-rep1.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide-0_min-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L465-Diamide-0_min-rep2/Diamide-0_min-rep2_S22_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L465-Diamide-0_min-rep2/L465-Diamide-0_min-rep2.181008_NB551514_0042_AH2JJGBGX9.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L465-Diamide-0_min-rep2/L465-Diamide-0_min-rep2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L465-Diamide-0_min-rep2/Diamide-0_min-rep2_S22_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L465-Diamide-0_min-rep2/L465-Diamide-0_min-rep2.181008_NB551514_0042_AH2JJGBGX9.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L465-Diamide-0_min-rep2/L465-Diamide-0_min-rep2.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide-0_min-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L466-Diamide-15_min-rep1/Diamide-15_min-rep1_S23_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L466-Diamide-15_min-rep1/L466-Diamide-15_min-rep1.181008_NB551514_0042_AH2JJGBGX9.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L466-Diamide-15_min-rep1/L466-Diamide-15_min-rep1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L466-Diamide-15_min-rep1/Diamide-15_min-rep1_S23_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L466-Diamide-15_min-rep1/L466-Diamide-15_min-rep1.181008_NB551514_0042_AH2JJGBGX9.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L466-Diamide-15_min-rep1/L466-Diamide-15_min-rep1.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide-15_min-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L467-Diamide-15_min-rep2/Diamide-15_min-rep2_S24_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L467-Diamide-15_min-rep2/L467-Diamide-15_min-rep2.181008_NB551514_0042_AH2JJGBGX9.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L467-Diamide-15_min-rep2/L467-Diamide-15_min-rep2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L467-Diamide-15_min-rep2/Diamide-15_min-rep2_S24_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L467-Diamide-15_min-rep2/L467-Diamide-15_min-rep2.181008_NB551514_0042_AH2JJGBGX9.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L467-Diamide-15_min-rep2/L467-Diamide-15_min-rep2.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide-15_min-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L468-Diamide-30_min-rep1/Diamide-30_min-rep1_S25_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L468-Diamide-30_min-rep1/L468-Diamide-30_min-rep1.181008_NB551514_0042_AH2JJGBGX9.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L468-Diamide-30_min-rep1/L468-Diamide-30_min-rep1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L468-Diamide-30_min-rep1/Diamide-30_min-rep1_S25_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L468-Diamide-30_min-rep1/L468-Diamide-30_min-rep1.181008_NB551514_0042_AH2JJGBGX9.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L468-Diamide-30_min-rep1/L468-Diamide-30_min-rep1.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide-30_min-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L469-Diamide-30_min-rep2/Diamide-30_min-rep2_S26_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L469-Diamide-30_min-rep2/L469-Diamide-30_min-rep2.181008_NB551514_0042_AH2JJGBGX9.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L469-Diamide-30_min-rep2/L469-Diamide-30_min-rep2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L469-Diamide-30_min-rep2/Diamide-30_min-rep2_S26_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L469-Diamide-30_min-rep2/L469-Diamide-30_min-rep2.181008_NB551514_0042_AH2JJGBGX9.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L469-Diamide-30_min-rep2/L469-Diamide-30_min-rep2.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide-30_min-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L470-Diamide-45_min-rep1/Diamide-45_min-rep1_S27_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L470-Diamide-45_min-rep1/L470-Diamide-45_min-rep1.181008_NB551514_0042_AH2JJGBGX9.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L470-Diamide-45_min-rep1/L470-Diamide-45_min-rep1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L470-Diamide-45_min-rep1/Diamide-45_min-rep1_S27_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L470-Diamide-45_min-rep1/L470-Diamide-45_min-rep1.181008_NB551514_0042_AH2JJGBGX9.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L470-Diamide-45_min-rep1/L470-Diamide-45_min-rep1.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide-45_min-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L471-Diamide-45_min-rep2/Diamide-45_min-rep2_S28_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L471-Diamide-45_min-rep2/L471-Diamide-45_min-rep2.181008_NB551514_0042_AH2JJGBGX9.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L471-Diamide-45_min-rep2/L471-Diamide-45_min-rep2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L471-Diamide-45_min-rep2/Diamide-45_min-rep2_S28_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L471-Diamide-45_min-rep2/L471-Diamide-45_min-rep2.181008_NB551514_0042_AH2JJGBGX9.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L471-Diamide-45_min-rep2/L471-Diamide-45_min-rep2.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide-45_min-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L472-Diamide-60_min-rep1/Diamide-60_min-rep1_S29_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L472-Diamide-60_min-rep1/L472-Diamide-60_min-rep1.181008_NB551514_0042_AH2JJGBGX9.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L472-Diamide-60_min-rep1/L472-Diamide-60_min-rep1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L472-Diamide-60_min-rep1/Diamide-60_min-rep1_S29_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L472-Diamide-60_min-rep1/L472-Diamide-60_min-rep1.181008_NB551514_0042_AH2JJGBGX9.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L472-Diamide-60_min-rep1/L472-Diamide-60_min-rep1.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide-60_min-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L473-Diamide-60_min-rep2/Diamide-60_min-rep2_S30_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L473-Diamide-60_min-rep2/L473-Diamide-60_min-rep2.181008_NB551514_0042_AH2JJGBGX9.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L473-Diamide-60_min-rep2/L473-Diamide-60_min-rep2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L473-Diamide-60_min-rep2/Diamide-60_min-rep2_S30_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L473-Diamide-60_min-rep2/L473-Diamide-60_min-rep2.181008_NB551514_0042_AH2JJGBGX9.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L473-Diamide-60_min-rep2/L473-Diamide-60_min-rep2.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide-60_min-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py Diamide_Hsf_0_S6_R1_001.50mers.fastq.gz Diamide_Hsf_0_S6_R2_001.50mers.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide_Hsf_0.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py Diamide_Hsf_30_S7_R1_001.50mers.fastq.gz Diamide_Hsf_30_S7_R2_001.50mers.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide_Hsf_30.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py Diamide_Hsf_60_S8_R1_001.50mers.fastq.gz Diamide_Hsf_60_S8_R2_001.50mers.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - Diamide_Hsf_60.2x36mers.unique