python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-0_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-0_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-0_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-0_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-0_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-0_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24h_24h_washout_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24h_24h_washout_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24h_24h_washout_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24h_24h_washout_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24h_24h_washout_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24h_24h_washout_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-3_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-3_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-3_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-3_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-3_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-3_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-0_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-0_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-0_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-0_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-0_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-0_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24h_24h_washout_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24h_24h_washout_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24h_24h_washout_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24h_24h_washout_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24h_24h_washout_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24h_24h_washout_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-3_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-3_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-3_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-3_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-3_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-3_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-0_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-0_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-0_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-0_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-0_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-0_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24h_24h_washout_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24h_24h_washout_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24h_24h_washout_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24h_24h_washout_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24h_24h_washout_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24h_24h_washout_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-3_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-3_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-3_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-3_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-3_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-3_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-0_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-0_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-0_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-0_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-0_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-0_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24h_24h_washout_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24h_24h_washout_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24h_24h_washout_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24h_24h_washout_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24h_24h_washout_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24h_24h_washout_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-3_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-3_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-3_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-3_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-3_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-3_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-0_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-0_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-0_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-0_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-0_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-0_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24h_24h_washout_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24h_24h_washout_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24h_24h_washout_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24h_24h_washout_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24h_24h_washout_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24h_24h_washout_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-3_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-3_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-3_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-3_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-3_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-3_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-0_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-0_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-0_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-0_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-0_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-0_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24h_24h_washout_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24h_24h_washout_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24h_24h_washout_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24h_24h_washout_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24h_24h_washout_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24h_24h_washout_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-3_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-3_hour_rep1.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-3_hour_rep1.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-3_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-3_hour_rep2.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/hg20/bowtie-indexes/chrM -p 8 -v 2 -a -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/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-3_hour_rep2.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-0_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-0_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-0_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-0_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-0_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-0_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24h_24h_washout_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24h_24h_washout_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24h_24h_washout_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24h_24h_washout_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24h_24h_washout_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24h_24h_washout_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-24_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-3_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-3_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-3_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-3_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-3_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-ASCL1_guide-3_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-0_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-0_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-0_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-0_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-0_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-0_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24h_24h_washout_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24h_24h_washout_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24h_24h_washout_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24h_24h_washout_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24h_24h_washout_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24h_24h_washout_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-24_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-3_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-3_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-3_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-3_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-3_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-guide_virus-3_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-0_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-0_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-0_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-0_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-0_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-0_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24h_24h_washout_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24h_24h_washout_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24h_24h_washout_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24h_24h_washout_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24h_24h_washout_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24h_24h_washout_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-24_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-3_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-3_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-3_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-3_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-3_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VP64-no_guide-3_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-0_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-0_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-0_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-0_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-0_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-0_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24h_24h_washout_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24h_24h_washout_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24h_24h_washout_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24h_24h_washout_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24h_24h_washout_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24h_24h_washout_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-24_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-3_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-3_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-3_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-3_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-3_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-ASCL1_guide-3_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-0_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-0_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-0_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-0_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-0_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-0_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24h_24h_washout_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24h_24h_washout_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24h_24h_washout_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24h_24h_washout_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24h_24h_washout_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24h_24h_washout_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-24_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-3_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-3_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-3_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-3_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-3_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-guide_virus-3_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-0_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-0_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-0_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-0_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-0_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-0_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24h_24h_washout_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24h_24h_washout_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24h_24h_washout_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24h_24h_washout_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24h_24h_washout_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24h_24h_washout_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-24_hour_rep2.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-3_hour_rep1.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-3_hour_rep1.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-3_hour_rep1.2x36mers.hg38-female.unique
python ~/code/PEFastqToTabDelimited.py 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-3_hour_rep2.end1.fastq.gz 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-3_hour_rep2.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/hg20/bowtie-indexes/hg38-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 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-29_PATAC_HEK293_ASCL1-VPR-no_guide-3_hour_rep2.2x36mers.hg38-female.unique