python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L285-Tn5_test_1/Tn5_test_1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L285-Tn5_test_1/Tn5_test_1.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -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/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L285-Tn5_test_1.2x25mers.E_coli.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L286-Tn5_test_2/Tn5_test_2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L286-Tn5_test_2/Tn5_test_2.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -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/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L286-Tn5_test_2.2x25mers.E_coli.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L287-Tn5_test_3/Tn5_test_3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L287-Tn5_test_3/Tn5_test_3.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -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/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L287-Tn5_test_3.2x25mers.E_coli.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L288-Tn5_test_4/Tn5_test_4.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L288-Tn5_test_4/Tn5_test_4.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -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/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L288-Tn5_test_4.2x25mers.E_coli.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L285-Tn5_test_1/Tn5_test_1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L285-Tn5_test_1/Tn5_test_1.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9 -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/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L285-Tn5_test_1.2x25mers.mm9.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L286-Tn5_test_2/Tn5_test_2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L286-Tn5_test_2/Tn5_test_2.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9 -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/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L286-Tn5_test_2.2x25mers.mm9.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L287-Tn5_test_3/Tn5_test_3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L287-Tn5_test_3/Tn5_test_3.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9 -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/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L287-Tn5_test_3.2x25mers.mm9.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L288-Tn5_test_4/Tn5_test_4.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L288-Tn5_test_4/Tn5_test_4.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9 -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/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L288-Tn5_test_4.2x25mers.mm9.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L285-Tn5_test_1/Tn5_test_1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L285-Tn5_test_1/Tn5_test_1.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19 -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/hg19/bowtie-indexes/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L285-Tn5_test_1.2x25mers.hg19.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L286-Tn5_test_2/Tn5_test_2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L286-Tn5_test_2/Tn5_test_2.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19 -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/hg19/bowtie-indexes/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L286-Tn5_test_2.2x25mers.hg19.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L287-Tn5_test_3/Tn5_test_3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L287-Tn5_test_3/Tn5_test_3.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19 -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/hg19/bowtie-indexes/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L287-Tn5_test_3.2x25mers.hg19.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L288-Tn5_test_4/Tn5_test_4.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L288-Tn5_test_4/Tn5_test_4.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19 -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/hg19/bowtie-indexes/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L288-Tn5_test_4.2x25mers.hg19.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L285-Tn5_test_1/Tn5_test_1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L285-Tn5_test_1/Tn5_test_1.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L285-Tn5_test_1.2x25mers.sacCer3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L286-Tn5_test_2/Tn5_test_2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L286-Tn5_test_2/Tn5_test_2.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L286-Tn5_test_2.2x25mers.sacCer3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L287-Tn5_test_3/Tn5_test_3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L287-Tn5_test_3/Tn5_test_3.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L287-Tn5_test_3.2x25mers.sacCer3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L288-Tn5_test_4/Tn5_test_4.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L288-Tn5_test_4/Tn5_test_4.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L288-Tn5_test_4.2x25mers.sacCer3.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L285-Tn5_test_1/Tn5_test_1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L285-Tn5_test_1/Tn5_test_1.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -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/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L285-Tn5_test_1.2x25mers.dm6.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L286-Tn5_test_2/Tn5_test_2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L286-Tn5_test_2/Tn5_test_2.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -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/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L286-Tn5_test_2.2x25mers.dm6.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L287-Tn5_test_3/Tn5_test_3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L287-Tn5_test_3/Tn5_test_3.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -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/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L287-Tn5_test_3.2x25mers.dm6.unique
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L288-Tn5_test_4/Tn5_test_4.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L288-Tn5_test_4/Tn5_test_4.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -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/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L288-Tn5_test_4.2x25mers.dm6.unique