python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L194-S2-ATAC-rep1/S2_ATAC_1_R1_trimmed.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L194-S2-ATAC-rep1/S2_ATAC_1_R2_trimmed.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L194-S2-ATAC-rep1.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L195-S2-ATAC-rep2/S2_ATAC_2_R1_trimmed.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L195-S2-ATAC-rep2/S2_ATAC_2_R2_trimmed.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L195-S2-ATAC-rep2.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L209-S2_Ecd_0h_Rep1/S2_Ecd_0h_Rep1_S1_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L209-S2_Ecd_0h_Rep1/S2_Ecd_0h_Rep1_S1_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L209-S2_Ecd_0h_Rep1.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L210-S2_Ecd_0h_Rep2/S2_Ecd_0h_Rep2_S2_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L210-S2_Ecd_0h_Rep2/S2_Ecd_0h_Rep2_S2_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L210-S2_Ecd_0h_Rep2.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L211-S2_Ecd_2h_Rep1/S2_Ecd_2h_Rep1_S3_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L211-S2_Ecd_2h_Rep1/S2_Ecd_2h_Rep1_S3_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L211-S2_Ecd_2h_Rep1.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L212-S2_Ecd_2h_Rep2/S2_Ecd_2h_Rep2_S4_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L212-S2_Ecd_2h_Rep2/S2_Ecd_2h_Rep2_S4_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L212-S2_Ecd_2h_Rep2.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L213-S2_Ecd_4h_Rep1/S2_Ecd_4h_Rep1_S5_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L213-S2_Ecd_4h_Rep1/S2_Ecd_4h_Rep1_S5_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L213-S2_Ecd_4h_Rep1.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L214-S2_Ecd_4h_Rep2/S2_Ecd_4h_Rep2_S6_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L214-S2_Ecd_4h_Rep2/S2_Ecd_4h_Rep2_S6_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L214-S2_Ecd_4h_Rep2.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L215-S2_Ecd_8h_Rep1/S2_Ecd_8h_Rep1_S7_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L215-S2_Ecd_8h_Rep1/S2_Ecd_8h_Rep1_S7_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L215-S2_Ecd_8h_Rep1.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L216-S2_Ecd_8h_Rep2/S2_Ecd_8h_Rep2_S8_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L216-S2_Ecd_8h_Rep2/S2_Ecd_8h_Rep2_S8_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L216-S2_Ecd_8h_Rep2.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L217-S2_Ecd_12h_Rep1/S2_Ecd_12h_Rep1_S9_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L217-S2_Ecd_12h_Rep1/S2_Ecd_12h_Rep1_S9_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L217-S2_Ecd_12h_Rep1.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L218-S2_Ecd_12h_Rep2/S2_Ecd_12h_Rep2_S10_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L218-S2_Ecd_12h_Rep2/S2_Ecd_12h_Rep2_S10_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L218-S2_Ecd_12h_Rep2.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L219-S2_Ecd_24h_Rep1/S2_Ecd_24h_Rep1_S11_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L219-S2_Ecd_24h_Rep1/S2_Ecd_24h_Rep1_S11_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L219-S2_Ecd_24h_Rep1.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L220-S2_Ecd_24h_Rep2/S2_Ecd_24h_Rep2_S12_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L220-S2_Ecd_24h_Rep2/S2_Ecd_24h_Rep2_S12_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L220-S2_Ecd_24h_Rep2.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L221-S2_no_Ecd_24h_Rep1/S2_no_Ecd_24h_Rep1_S13_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L221-S2_no_Ecd_24h_Rep1/S2_no_Ecd_24h_Rep1_S13_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L221-S2_no_Ecd_24h_Rep1.2x36mers.dm3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L222-S2_no_Ecd_24h_Rep2/S2_no_Ecd_24h_Rep2_S14_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L222-S2_no_Ecd_24h_Rep2/S2_no_Ecd_24h_Rep2_S14_R2_001.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/dm3/bowtie-indexes/dm3 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L222-S2_no_Ecd_24h_Rep2.2x36mers.dm3.unique