python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L300_S1_L001_R1_001.fastq.gz L300_S1_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L300-Archeal-ATAC-test-5M_cells-30min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L301_S2_L001_R1_001.fastq.gz L301_S2_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L301-Archeal-ATAC-test-50M_cells-30min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L302_S3_L001_R1_001.fastq.gz L302_S3_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L302-Archeal-ATAC-test-500M_cells-30min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L303_S4_L001_R1_001.fastq.gz L303_S4_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L303-Archeal-ATAC-test-5M_cells-Tween-30min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L304_S5_L001_R1_001.fastq.gz L304_S5_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L304-Archeal-ATAC-test-50M_cells-Tween-30min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L305_S6_L001_R1_001.fastq.gz L305_S6_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L305-Archeal-ATAC-test-500M_cells-Tween-30min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L306_S7_L001_R1_001.fastq.gz L306_S7_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L306-Archeal-ATAC-test-5M_cells-Tween-Digi-30min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L307_S8_L001_R1_001.fastq.gz L307_S8_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L307-Archeal-ATAC-test-50M_cells-Tween-Digi-30min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L308_S9_L001_R1_001.fastq.gz L308_S9_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L308-Archeal-ATAC-test-500M_cells-Tween-Digi-30min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L309_S10_L001_R1_001.fastq.gz L309_S10_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L309-Archeal-ATAC-test-5M_cells-10min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L310_S11_L001_R1_001.fastq.gz L310_S11_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L310-Archeal-ATAC-test-50M_cells-10min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L311_S12_L001_R1_001.fastq.gz L311_S12_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L311-Archeal-ATAC-test-500M_cells-10min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L312_S13_L001_R1_001.fastq.gz L312_S13_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L312-Archeal-ATAC-test-5M_cells-Tween-10min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L313_S14_L001_R1_001.fastq.gz L313_S14_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L313-Archeal-ATAC-test-50M_cells-Tween-10min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L314_S15_L001_R1_001.fastq.gz L314_S15_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L314-Archeal-ATAC-test-500M_cells-Tween-10min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L315_S16_L001_R1_001.fastq.gz L315_S16_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L315-Archeal-ATAC-test-5M_cells-Tween-Digi-10min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L316_S17_L001_R1_001.fastq.gz L316_S17_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L316-Archeal-ATAC-test-50M_cells-Tween-Digi-10min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L317_S18_L001_R1_001.fastq.gz L317_S18_L001_R2_001.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -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 ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L317-Archeal-ATAC-test-500M_cells-Tween-Digi-10min.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L278_S19_L001_R1_001.fastq.gz L278_S19_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/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 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L278-diamide_0min_rep1.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L279_S20_L001_R1_001.fastq.gz L279_S20_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/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 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L279-diamide_15min_rep1.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L280_S21_L001_R1_001.fastq.gz L280_S21_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/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 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L280-diamide_30min_rep1.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L281_S22_L001_R1_001.fastq.gz L281_S22_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/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 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L281-diamide_0min_rep2.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L282_S23_L001_R1_001.fastq.gz L282_S23_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/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 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L282-diamide_15min_rep2.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L283_S24_L001_R1_001.fastq.gz L283_S24_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/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 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L283-diamide_30min_rep2.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMAfterTn5AB-GM-OATAC-a_S27_L001_R1_001.fastq.gz QC-HMAfterTn5AB-GM-OATAC-a_S27_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMAfterTn5AB-GM-OATAC-a.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMAfterTn5AB-GM-OATAC-b_S28_L001_R1_001.fastq.gz QC-HMAfterTn5AB-GM-OATAC-b_S28_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMAfterTn5AB-GM-OATAC-b.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMAfterTn5AB-P-GM-OATAC-a_S31_L001_R1_001.fastq.gz QC-HMAfterTn5AB-P-GM-OATAC-a_S31_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMAfterTn5AB-P-GM-OATAC-a.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMAfterTn5AB-P-GM-OATAC-b_S32_L001_R1_001.fastq.gz QC-HMAfterTn5AB-P-GM-OATAC-b_S32_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMAfterTn5AB-P-GM-OATAC-b.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMBeforeTn5AB-GM-OATAC-a_S25_L001_R1_001.fastq.gz QC-HMBeforeTn5AB-GM-OATAC-a_S25_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMBeforeTn5AB-GM-OATAC-a.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMBeforeTn5AB-GM-OATAC-b_S26_L001_R1_001.fastq.gz QC-HMBeforeTn5AB-GM-OATAC-b_S26_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMBeforeTn5AB-GM-OATAC-b.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMBeforeTn5AB-P-GM-OATAC-a_S29_L001_R1_001.fastq.gz QC-HMBeforeTn5AB-P-GM-OATAC-a_S29_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMBeforeTn5AB-P-GM-OATAC-a.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMBeforeTn5AB-P-GM-OATAC-b_S30_L001_R1_001.fastq.gz QC-HMBeforeTn5AB-P-GM-OATAC-b_S30_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMBeforeTn5AB-P-GM-OATAC-b.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-IlluminaTn5-GM_S33_L001_R1_001.fastq.gz QC-IlluminaTn5-GM_S33_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-IlluminaTn5-GM.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-P-HMTn5-K562_S35_L001_R1_001.fastq.gz QC-P-HMTn5-K562_S35_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-P-HMTn5-K562.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-WJG-Tn5-K562_S34_L001_R1_001.fastq.gz QC-WJG-Tn5-K562_S34_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-WJG-Tn5-K562.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMAfterTn5AB-GM-OATAC-a_S27_L001_R1_001.fastq.gz QC-HMAfterTn5AB-GM-OATAC-a_S27_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/chrM -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMAfterTn5AB-GM-OATAC-a.2x36mers.hg19-chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMAfterTn5AB-GM-OATAC-b_S28_L001_R1_001.fastq.gz QC-HMAfterTn5AB-GM-OATAC-b_S28_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/chrM -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMAfterTn5AB-GM-OATAC-b.2x36mers.hg19-chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMAfterTn5AB-P-GM-OATAC-a_S31_L001_R1_001.fastq.gz QC-HMAfterTn5AB-P-GM-OATAC-a_S31_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/chrM -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMAfterTn5AB-P-GM-OATAC-a.2x36mers.hg19-chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMAfterTn5AB-P-GM-OATAC-b_S32_L001_R1_001.fastq.gz QC-HMAfterTn5AB-P-GM-OATAC-b_S32_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/chrM -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMAfterTn5AB-P-GM-OATAC-b.2x36mers.hg19-chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMBeforeTn5AB-GM-OATAC-a_S25_L001_R1_001.fastq.gz QC-HMBeforeTn5AB-GM-OATAC-a_S25_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/chrM -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMBeforeTn5AB-GM-OATAC-a.2x36mers.hg19-chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMBeforeTn5AB-GM-OATAC-b_S26_L001_R1_001.fastq.gz QC-HMBeforeTn5AB-GM-OATAC-b_S26_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/chrM -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMBeforeTn5AB-GM-OATAC-b.2x36mers.hg19-chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMBeforeTn5AB-P-GM-OATAC-a_S29_L001_R1_001.fastq.gz QC-HMBeforeTn5AB-P-GM-OATAC-a_S29_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/chrM -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMBeforeTn5AB-P-GM-OATAC-a.2x36mers.hg19-chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-HMBeforeTn5AB-P-GM-OATAC-b_S30_L001_R1_001.fastq.gz QC-HMBeforeTn5AB-P-GM-OATAC-b_S30_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/chrM -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-HMBeforeTn5AB-P-GM-OATAC-b.2x36mers.hg19-chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-IlluminaTn5-GM_S33_L001_R1_001.fastq.gz QC-IlluminaTn5-GM_S33_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/chrM -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-IlluminaTn5-GM.2x36mers.hg19-chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-P-HMTn5-K562_S35_L001_R1_001.fastq.gz QC-P-HMTn5-K562_S35_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/chrM -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-P-HMTn5-K562.2x36mers.hg19-chrM.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py QC-WJG-Tn5-K562_S34_L001_R1_001.fastq.gz QC-WJG-Tn5-K562_S34_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/chrM -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - QC-WJG-Tn5-K562.2x36mers.hg19-chrM.unique