python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1034-Training_camp_4-HOG1-0min-rep1-ajberg5/L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1034-Training_camp_4-HOG1-0min-rep1-ajberg5/L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1035-Training_camp_5-YAP1-0min-rep2-annashch/L1035-Training_camp_5-YAP1-0min-rep2-annashch.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1035-Training_camp_5-YAP1-0min-rep2-annashch/L1035-Training_camp_5-YAP1-0min-rep2-annashch.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1035-Training_camp_5-YAP1-0min-rep2-annashch.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1037-Training_camp_7-MSN2-0min-rep2-annlin/L1037-Training_camp_7-MSN2-0min-rep2-annlin.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1037-Training_camp_7-MSN2-0min-rep2-annlin/L1037-Training_camp_7-MSN2-0min-rep2-annlin.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1037-Training_camp_7-MSN2-0min-rep2-annlin.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1040-Training_camp_10-MSN4-0min-rep2-clin5/L1040-Training_camp_10-MSN4-0min-rep2-clin5.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1040-Training_camp_10-MSN4-0min-rep2-clin5/L1040-Training_camp_10-MSN4-0min-rep2-clin5.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1040-Training_camp_10-MSN4-0min-rep2-clin5.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1042-Training_camp_12-YAP1-0min-rep1-courtrun/L1042-Training_camp_12-YAP1-0min-rep1-courtrun.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1042-Training_camp_12-YAP1-0min-rep1-courtrun/L1042-Training_camp_12-YAP1-0min-rep1-courtrun.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1042-Training_camp_12-YAP1-0min-rep1-courtrun.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1043-Training_camp_13-MSN1-0min-rep2-cvduffy/L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1043-Training_camp_13-MSN1-0min-rep2-cvduffy/L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1045-Training_camp_15-WT-0min-rep1-genegra2/L1045-Training_camp_15-WT-0min-rep1-genegra2.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1045-Training_camp_15-WT-0min-rep1-genegra2/L1045-Training_camp_15-WT-0min-rep1-genegra2.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1045-Training_camp_15-WT-0min-rep1-genegra2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1048-Training_camp_18-SKN7-0min-rep2-jarhodes/L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1048-Training_camp_18-SKN7-0min-rep2-jarhodes/L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1050-Training_camp_20-MSN4-0min-rep1-lstrand/L1050-Training_camp_20-MSN4-0min-rep1-lstrand.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1050-Training_camp_20-MSN4-0min-rep1-lstrand/L1050-Training_camp_20-MSN4-0min-rep1-lstrand.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1050-Training_camp_20-MSN4-0min-rep1-lstrand.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1052-Training_camp_22-SKN7-0min-rep1-makena/L1052-Training_camp_22-SKN7-0min-rep1-makena.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1052-Training_camp_22-SKN7-0min-rep1-makena/L1052-Training_camp_22-SKN7-0min-rep1-makena.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1052-Training_camp_22-SKN7-0min-rep1-makena.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1055-Training_camp_26-HOG1-0min-rep2-miao1/L1055-Training_camp_26-HOG1-0min-rep2-miao1.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1055-Training_camp_26-HOG1-0min-rep2-miao1/L1055-Training_camp_26-HOG1-0min-rep2-miao1.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1055-Training_camp_26-HOG1-0min-rep2-miao1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1057-Training_camp_28-HOT1-0min-rep1-myhayes/L1057-Training_camp_28-HOT1-0min-rep1-myhayes.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1057-Training_camp_28-HOT1-0min-rep1-myhayes/L1057-Training_camp_28-HOT1-0min-rep1-myhayes.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1057-Training_camp_28-HOT1-0min-rep1-myhayes.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1058-Training_camp_29-MSN1-0min-rep1-sierrasb/L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1058-Training_camp_29-MSN1-0min-rep1-sierrasb/L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1061-Training_camp_32-HOT1-0min-rep2-soumyak/L1061-Training_camp_32-HOT1-0min-rep2-soumyak.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1061-Training_camp_32-HOT1-0min-rep2-soumyak/L1061-Training_camp_32-HOT1-0min-rep2-soumyak.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1061-Training_camp_32-HOT1-0min-rep2-soumyak.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1062-Training_camp_33-WT-0min-rep2-srstern/L1062-Training_camp_33-WT-0min-rep2-srstern.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1062-Training_camp_33-WT-0min-rep2-srstern/L1062-Training_camp_33-WT-0min-rep2-srstern.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1062-Training_camp_33-WT-0min-rep2-srstern.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1064-Training_camp_35-MSN2-0min-rep1-subkc/L1064-Training_camp_35-MSN2-0min-rep1-subkc.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1064-Training_camp_35-MSN2-0min-rep1-subkc/L1064-Training_camp_35-MSN2-0min-rep1-subkc.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1064-Training_camp_35-MSN2-0min-rep1-subkc.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1067-Training_camp_38-YAP7-0min-rep2-surag/L1067-Training_camp_38-YAP7-0min-rep2-surag.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1067-Training_camp_38-YAP7-0min-rep2-surag/L1067-Training_camp_38-YAP7-0min-rep2-surag.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1067-Training_camp_38-YAP7-0min-rep2-surag.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1068-Training_camp_39-YAP6-0min-rep2-zahoor/L1068-Training_camp_39-YAP6-0min-rep2-zahoor.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1068-Training_camp_39-YAP6-0min-rep2-zahoor/L1068-Training_camp_39-YAP6-0min-rep2-zahoor.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1068-Training_camp_39-YAP6-0min-rep2-zahoor.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L665-FUN30/L665-FUN30.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L665-FUN30/L665-FUN30.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L665-FUN30/L665-FUN30.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L665-FUN30/L665-FUN30.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L665-FUN30.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L666-MSS11/L666-MSS11.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L666-MSS11/L666-MSS11.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L666-MSS11.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L667-YAP7/L667-YAP7.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L667-YAP7/L667-YAP7.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L667-YAP7.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L668-CUP9/L668-CUP9.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L668-CUP9/L668-CUP9.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L668-CUP9/L668-CUP9.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L668-CUP9/L668-CUP9.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L668-CUP9.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L669-ARG80/L669-ARG80.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L669-ARG80/L669-ARG80.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L669-ARG80/L669-ARG80.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L669-ARG80/L669-ARG80.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L669-ARG80.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L670-ARP6/L670-ARP6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L670-ARP6/L670-ARP6.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L670-ARP6/L670-ARP6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L670-ARP6/L670-ARP6.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L670-ARP6.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L671-HAP5/L671-HAP5.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L671-HAP5/L671-HAP5.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L671-HAP5.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L672-CAT8/L672-CAT8.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L672-CAT8/L672-CAT8.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L672-CAT8.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L673-RDS2/L673-RDS2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L673-RDS2/L673-RDS2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L673-RDS2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L674-CIN5/L674-CIN5.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L674-CIN5/L674-CIN5.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L674-CIN5.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L675-RDR1/L675-RDR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L675-RDR1/L675-RDR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L675-RDR1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L676-AFT2/L676-AFT2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L676-AFT2/L676-AFT2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L676-AFT2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L677-YAP1/L677-YAP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L677-YAP1/L677-YAP1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L677-YAP1/L677-YAP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L677-YAP1/L677-YAP1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L677-YAP1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L678-IOC2/L678-IOC2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L678-IOC2/L678-IOC2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L678-IOC2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L679-MAC1/L679-MAC1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L679-MAC1/L679-MAC1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L679-MAC1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L680-RTG1/L680-RTG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L680-RTG1/L680-RTG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L680-RTG1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L681-RGM1/L681-RGM1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L681-RGM1/L681-RGM1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L681-RGM1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L682-ERT1/L682-ERT1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L682-ERT1/L682-ERT1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L682-ERT1/L682-ERT1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L682-ERT1/L682-ERT1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L682-ERT1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L683-TYE7/L683-TYE7.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L683-TYE7/L683-TYE7.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L683-TYE7.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L684-DAL82/L684-DAL82.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L684-DAL82/L684-DAL82.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L684-DAL82.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L685-TEA1/L685-TEA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L685-TEA1/L685-TEA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L685-TEA1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L686-USV1/L686-USV1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L686-USV1/L686-USV1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L686-USV1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L687-SMP1/L687-SMP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L687-SMP1/L687-SMP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L687-SMP1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L688-ABF2/L688-ABF2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L688-ABF2/L688-ABF2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L688-ABF2/L688-ABF2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L688-ABF2/L688-ABF2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L688-ABF2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L689-MBP1/L689-MBP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L689-MBP1/L689-MBP1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L689-MBP1/L689-MBP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L689-MBP1/L689-MBP1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L689-MBP1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L690-CRZ1/L690-CRZ1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L690-CRZ1/L690-CRZ1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L690-CRZ1/L690-CRZ1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L690-CRZ1/L690-CRZ1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L690-CRZ1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L691-FKH2/L691-FKH2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L691-FKH2/L691-FKH2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L691-FKH2/L691-FKH2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L691-FKH2/L691-FKH2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L691-FKH2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L692-GAT4/L692-GAT4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L692-GAT4/L692-GAT4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L692-GAT4/L692-GAT4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L692-GAT4/L692-GAT4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L692-GAT4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L693-STP4/L693-STP4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L693-STP4/L693-STP4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L693-STP4/L693-STP4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L693-STP4/L693-STP4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L693-STP4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L694-IOC3/L694-IOC3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L694-IOC3/L694-IOC3.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L694-IOC3/L694-IOC3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L694-IOC3/L694-IOC3.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L694-IOC3.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L695-NRG2/L695-NRG2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L695-NRG2/L695-NRG2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L695-NRG2/L695-NRG2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L695-NRG2/L695-NRG2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L695-NRG2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L697-CST9/L697-CST9.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L697-CST9/L697-CST9.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L697-CST9.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L698-CST6/L698-CST6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L698-CST6/L698-CST6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L698-CST6.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L699-WAR1/L699-WAR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L699-WAR1/L699-WAR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L699-WAR1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L701-DAL80/L701-DAL80.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L701-DAL80/L701-DAL80.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L701-DAL80.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L702-SIR2/L702-SIR2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L702-SIR2/L702-SIR2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L702-SIR2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L704-REC8/L704-REC8.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L704-REC8/L704-REC8.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L704-REC8.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L705-TBS1/L705-TBS1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L705-TBS1/L705-TBS1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L705-TBS1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L706-URC2/L706-URC2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L706-URC2/L706-URC2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L706-URC2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L708-HDA1/L708-HDA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L708-HDA1/L708-HDA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L708-HDA1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L710-ASG1/L710-ASG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L710-ASG1/L710-ASG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L710-ASG1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L713-YNR063W/L713-YNR063W.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L713-YNR063W/L713-YNR063W.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L713-YNR063W/L713-YNR063W.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L713-YNR063W/L713-YNR063W.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L713-YNR063W.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L716-HOG1/L716-HOG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L716-HOG1/L716-HOG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L716-HOG1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L717-DOT6/L717-DOT6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L717-DOT6/L717-DOT6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L717-DOT6.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L718-MSN1/L718-MSN1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L718-MSN1/L718-MSN1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L718-MSN1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L720-INO4/L720-INO4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L720-INO4/L720-INO4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L720-INO4/L720-INO4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L720-INO4/L720-INO4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L720-INO4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L721-BYE1/L721-BYE1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L721-BYE1/L721-BYE1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L721-BYE1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L722-LSM1/L722-LSM1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L722-LSM1/L722-LSM1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L722-LSM1/L722-LSM1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L722-LSM1/L722-LSM1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L722-LSM1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L723-YER064C/L723-YER064C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L723-YER064C/L723-YER064C.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L723-YER064C/L723-YER064C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L723-YER064C/L723-YER064C.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L723-YER064C.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L725-YFL052W/L725-YFL052W.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L725-YFL052W/L725-YFL052W.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L725-YFL052W/L725-YFL052W.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L725-YFL052W/L725-YFL052W.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L725-YFL052W.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L726-HAL9/L726-HAL9.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L726-HAL9/L726-HAL9.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L726-HAL9/L726-HAL9.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L726-HAL9/L726-HAL9.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L726-HAL9.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L727-RPH1/L727-RPH1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L727-RPH1/L727-RPH1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L727-RPH1/L727-RPH1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L727-RPH1/L727-RPH1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L727-RPH1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L730-GAT1/L730-GAT1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L730-GAT1/L730-GAT1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L730-GAT1/L730-GAT1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L730-GAT1/L730-GAT1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L730-GAT1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L732-YER130C/L732-YER130C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L732-YER130C/L732-YER130C.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L732-YER130C/L732-YER130C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L732-YER130C/L732-YER130C.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L732-YER130C.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L733-RTG3/L733-RTG3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L733-RTG3/L733-RTG3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L733-RTG3.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L734-SWI4/L734-SWI4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L734-SWI4/L734-SWI4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L734-SWI4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L735-RPN4/L735-RPN4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L735-RPN4/L735-RPN4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L735-RPN4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L736-SPO11/L736-SPO11.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L736-SPO11/L736-SPO11.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L736-SPO11.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L737-STB5/L737-STB5.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L737-STB5/L737-STB5.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L737-STB5.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L738-NDT80/L738-NDT80.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L738-NDT80/L738-NDT80.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L738-NDT80.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L739-GIS1/L739-GIS1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L739-GIS1/L739-GIS1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L739-GIS1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L740-LEU3/L740-LEU3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L740-LEU3/L740-LEU3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L740-LEU3.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L741-YAP3/L741-YAP3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L741-YAP3/L741-YAP3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L741-YAP3.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L742-NRG1/L742-NRG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L742-NRG1/L742-NRG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L742-NRG1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L743-MSN4/L743-MSN4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L743-MSN4/L743-MSN4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L743-MSN4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L744-ASH1/L744-ASH1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L744-ASH1/L744-ASH1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L744-ASH1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L745-HAP4/L745-HAP4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L745-HAP4/L745-HAP4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L745-HAP4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L746-HPC2/L746-HPC2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L746-HPC2/L746-HPC2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L746-HPC2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L747-TOS8/L747-TOS8.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L747-TOS8/L747-TOS8.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L747-TOS8.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L748-HOT1/L748-HOT1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L748-HOT1/L748-HOT1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L748-HOT1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L749-KAR4/L749-KAR4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L749-KAR4/L749-KAR4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L749-KAR4/L749-KAR4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L749-KAR4/L749-KAR4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L749-KAR4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L750-AZF1/L750-AZF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L750-AZF1/L750-AZF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L750-AZF1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L751-ELG1/L751-ELG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L751-ELG1/L751-ELG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L751-ELG1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L752-YGR067C/L752-YGR067C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L752-YGR067C/L752-YGR067C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L752-YGR067C.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L753-unknown/L753-unknown.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L753-unknown/L753-unknown.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L753-unknown.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L754-LYS14/L754-LYS14.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L754-LYS14/L754-LYS14.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L754-LYS14.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L755-HIR3/L755-HIR3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L755-HIR3/L755-HIR3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L755-HIR3.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L756-STB4/L756-STB4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L756-STB4/L756-STB4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L756-STB4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L757-KTI12/L757-KTI12.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L757-KTI12/L757-KTI12.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L757-KTI12.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L758-SKN7/L758-SKN7.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L758-SKN7/L758-SKN7.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L758-SKN7.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L759-RME1/L759-RME1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L759-RME1/L759-RME1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L759-RME1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L760-ISW1/L760-ISW1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L760-ISW1/L760-ISW1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L760-ISW1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L761-FZF1/L761-FZF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L761-FZF1/L761-FZF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L761-FZF1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L762-SIP4/L762-SIP4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L762-SIP4/L762-SIP4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L762-SIP4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L763-PUT3/L763-PUT3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L763-PUT3/L763-PUT3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L763-PUT3.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L764-STP2/L764-STP2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L764-STP2/L764-STP2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L764-STP2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L765-GZF3/L765-GZF3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L765-GZF3/L765-GZF3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L765-GZF3.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L766-BAS1/L766-BAS1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L766-BAS1/L766-BAS1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L766-BAS1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L767-SUT2/L767-SUT2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L767-SUT2/L767-SUT2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L767-SUT2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L768-ROX1/L768-ROX1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L768-ROX1/L768-ROX1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L768-ROX1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L769-LIF1/L769-LIF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L769-LIF1/L769-LIF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L769-LIF1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L770-THO1/L770-THO1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L770-THO1/L770-THO1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L770-THO1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L771-HDA2/L771-HDA2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L771-HDA2/L771-HDA2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L771-HDA2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L772-NUP170/L772-NUP170.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L772-NUP170/L772-NUP170.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L772-NUP170.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L773-YPR015C/L773-YPR015C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L773-YPR015C/L773-YPR015C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L773-YPR015C.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L774-SUB1/L774-SUB1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L774-SUB1/L774-SUB1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L774-SUB1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L775-IME1/L775-IME1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L775-IME1/L775-IME1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L775-IME1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L776-HIR1/L776-HIR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L776-HIR1/L776-HIR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L776-HIR1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L777-MET32/L777-MET32.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L777-MET32/L777-MET32.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L777-MET32.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L778-RLM1/L778-RLM1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L778-RLM1/L778-RLM1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L778-RLM1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L779-YTA7/L779-YTA7.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L779-YTA7/L779-YTA7.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L779-YTA7.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L780-HIR2/L780-HIR2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L780-HIR2/L780-HIR2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L780-HIR2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L781-ZAP1/L781-ZAP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L781-ZAP1/L781-ZAP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L781-ZAP1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L782-RDS1/L782-RDS1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L782-RDS1/L782-RDS1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L782-RDS1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L783-BDF1/L783-BDF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L783-BDF1/L783-BDF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L783-BDF1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L784-HDA3/L784-HDA3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L784-HDA3/L784-HDA3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L784-HDA3.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L785-CAD1/L785-CAD1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L785-CAD1/L785-CAD1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L785-CAD1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L786-SIR4/L786-SIR4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L786-SIR4/L786-SIR4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L786-SIR4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L787-REF2/L787-REF2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L787-REF2/L787-REF2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L787-REF2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L788-MET31/L788-MET31.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L788-MET31/L788-MET31.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L788-MET31.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L789-ARO80/L789-ARO80.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L789-ARO80/L789-ARO80.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L789-ARO80.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L790-RSF2/L790-RSF2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L790-RSF2/L790-RSF2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L790-RSF2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L791-CTF4/L791-CTF4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L791-CTF4/L791-CTF4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L791-CTF4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L792-CDC73/L792-CDC73.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L792-CDC73/L792-CDC73.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L792-CDC73.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L793-OAF1/L793-OAF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L793-OAF1/L793-OAF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L793-OAF1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L794-UPC2/L794-UPC2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L794-UPC2/L794-UPC2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L794-UPC2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L795-MIG3/L795-MIG3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L795-MIG3/L795-MIG3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L795-MIG3.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L796-UME6/L796-UME6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L796-UME6/L796-UME6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L796-UME6.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L797-REI1/L797-REI1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L797-REI1/L797-REI1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L797-REI1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L798-YLR278C/L798-YLR278C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L798-YLR278C/L798-YLR278C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L798-YLR278C.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L799-SFP1/L799-SFP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L799-SFP1/L799-SFP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L799-SFP1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L800-ECM23/L800-ECM23.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L800-ECM23/L800-ECM23.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L800-ECM23.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L801-VHR1/L801-VHR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L801-VHR1/L801-VHR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L801-VHR1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L802-DHH1/L802-DHH1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L802-DHH1/L802-DHH1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L802-DHH1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L803-YAP6/L803-YAP6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L803-YAP6/L803-YAP6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L803-YAP6.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L804-GCN4/L804-GCN4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L804-GCN4/L804-GCN4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L804-GCN4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L805-PDR1/L805-PDR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L805-PDR1/L805-PDR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L805-PDR1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L806-MIG2/L806-MIG2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L806-MIG2/L806-MIG2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L806-MIG2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L807-ADR1/L807-ADR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L807-ADR1/L807-ADR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L807-ADR1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L808-YPR022C/L808-YPR022C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L808-YPR022C/L808-YPR022C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L808-YPR022C.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L809-HAA1/L809-HAA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L809-HAA1/L809-HAA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L809-HAA1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L810-ARR1/L810-ARR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L810-ARR1/L810-ARR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L810-ARR1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L811-YPR013C/L811-YPR013C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L811-YPR013C/L811-YPR013C.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L811-YPR013C/L811-YPR013C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L811-YPR013C/L811-YPR013C.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L811-YPR013C.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L812-RGT1/L812-RGT1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L812-RGT1/L812-RGT1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L812-RGT1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L813-RFX1/L813-RFX1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L813-RFX1/L813-RFX1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L813-RFX1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L814-IXR1/L814-IXR1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L814-IXR1/L814-IXR1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L814-IXR1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L815-PDR8/L815-PDR8.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L815-PDR8/L815-PDR8.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L815-PDR8.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L816-ECM22/L816-ECM22.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L816-ECM22/L816-ECM22.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L816-ECM22.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L817-XRN1/L817-XRN1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L817-XRN1/L817-XRN1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L817-XRN1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L818-YRR1/L818-YRR1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L818-YRR1/L818-YRR1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L818-YRR1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L819-MSN2/L819-MSN2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L819-MSN2/L819-MSN2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L819-MSN2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L820-YPR196W/L820-YPR196W.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L820-YPR196W/L820-YPR196W.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L820-YPR196W.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L821-DAL81/L821-DAL81.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L821-DAL81/L821-DAL81.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L821-DAL81.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L822-HAT1/L822-HAT1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L822-HAT1/L822-HAT1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L822-HAT1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L823-PAF1/L823-PAF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L823-PAF1/L823-PAF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L823-PAF1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L824-NHP10/L824-NHP10.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L824-NHP10/L824-NHP10.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L824-NHP10.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L825-SPP1/L825-SPP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L825-SPP1/L825-SPP1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L825-SPP1/L825-SPP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L825-SPP1/L825-SPP1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L825-SPP1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L826-SFL1/L826-SFL1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L826-SFL1/L826-SFL1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L826-SFL1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L827-STP3/L827-STP3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L827-STP3/L827-STP3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L827-STP3.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L828-YRM1/L828-YRM1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L828-YRM1/L828-YRM1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L828-YRM1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L829-ISW2/L829-ISW2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L829-ISW2/L829-ISW2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L829-ISW2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L830-HTZ1/L830-HTZ1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L830-HTZ1/L830-HTZ1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L830-HTZ1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L831-PHD1/L831-PHD1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L831-PHD1/L831-PHD1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L831-PHD1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L832-SWI5/L832-SWI5.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L832-SWI5/L832-SWI5.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L832-SWI5/L832-SWI5.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L832-SWI5/L832-SWI5.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L832-SWI5.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L833-ACA1/L833-ACA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L833-ACA1/L833-ACA1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L833-ACA1/L833-ACA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L833-ACA1/L833-ACA1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L833-ACA1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L834-INO2/L834-INO2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L834-INO2/L834-INO2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L834-INO2/L834-INO2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L834-INO2/L834-INO2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L834-INO2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L835-PHO4/L835-PHO4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L835-PHO4/L835-PHO4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L835-PHO4/L835-PHO4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L835-PHO4/L835-PHO4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L835-PHO4.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L836-MGA1/L836-MGA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L836-MGA1/L836-MGA1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L836-MGA1/L836-MGA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L836-MGA1/L836-MGA1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L836-MGA1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L837-MIG1/L837-MIG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L837-MIG1/L837-MIG1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L837-MIG1/L837-MIG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L837-MIG1/L837-MIG1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L837-MIG1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L838-HAP3/L838-HAP3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L838-HAP3/L838-HAP3.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L838-HAP3/L838-HAP3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L838-HAP3/L838-HAP3.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L838-HAP3.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L839-YHR177W/L839-YHR177W.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L839-YHR177W/L839-YHR177W.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L839-YHR177W/L839-YHR177W.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L839-YHR177W/L839-YHR177W.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L839-YHR177W.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L847-GLN3/L847-GLN3.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L847-GLN3/L847-GLN3.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L847-GLN3.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L848-TOD6/L848-TOD6.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L848-TOD6/L848-TOD6.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L848-TOD6.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L925-MSN2-0min-rep1/L925-MSN2-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L925-MSN2-0min-rep1/L925-MSN2-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L925-MSN2-0min-rep1/L925-MSN2-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L925-MSN2-0min-rep1/L925-MSN2-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L925-MSN2-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L927-MSN1-0min-rep1/L927-MSN1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L927-MSN1-0min-rep1/L927-MSN1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L927-MSN1-0min-rep1/L927-MSN1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L927-MSN1-0min-rep1/L927-MSN1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L927-MSN1-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L928-HOG1-0min-rep1/L928-HOG1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L928-HOG1-0min-rep1/L928-HOG1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L928-HOG1-0min-rep1/L928-HOG1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L928-HOG1-0min-rep1/L928-HOG1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L928-HOG1-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L929-BDF1-0min-rep1/L929-BDF1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L929-BDF1-0min-rep1/L929-BDF1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L929-BDF1-0min-rep1/L929-BDF1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L929-BDF1-0min-rep1/L929-BDF1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L929-BDF1-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L930-YAP7-0min-rep1/L930-YAP7-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L930-YAP7-0min-rep1/L930-YAP7-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L930-YAP7-0min-rep1/L930-YAP7-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L930-YAP7-0min-rep1/L930-YAP7-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L930-YAP7-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L931-UME6-0min-rep1/L931-UME6-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L931-UME6-0min-rep1/L931-UME6-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L931-UME6-0min-rep1/L931-UME6-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L931-UME6-0min-rep1/L931-UME6-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L931-UME6-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L932-SMP1-0min-rep1/L932-SMP1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L932-SMP1-0min-rep1/L932-SMP1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L932-SMP1-0min-rep1/L932-SMP1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L932-SMP1-0min-rep1/L932-SMP1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L932-SMP1-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L933-YAP1-0min-rep1/L933-YAP1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L933-YAP1-0min-rep1/L933-YAP1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L933-YAP1-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L934-YAP3-0min-rep1/L934-YAP3-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L934-YAP3-0min-rep1/L934-YAP3-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L934-YAP3-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L935-ARR1-0min-rep1/L935-ARR1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L935-ARR1-0min-rep1/L935-ARR1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L935-ARR1-0min-rep1/L935-ARR1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L935-ARR1-0min-rep1/L935-ARR1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L935-ARR1-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L936-PHO4-0min-rep1/L936-PHO4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L936-PHO4-0min-rep1/L936-PHO4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L936-PHO4-0min-rep1/L936-PHO4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L936-PHO4-0min-rep1/L936-PHO4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L936-PHO4-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L937-YAP6-0min-rep1/L937-YAP6-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L937-YAP6-0min-rep1/L937-YAP6-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L937-YAP6-0min-rep1/L937-YAP6-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L937-YAP6-0min-rep1/L937-YAP6-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L937-YAP6-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L938-PDR3-0min-rep1/L938-PDR3-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L938-PDR3-0min-rep1/L938-PDR3-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L938-PDR3-0min-rep1/L938-PDR3-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L938-PDR3-0min-rep1/L938-PDR3-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L938-PDR3-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L939-GAT1-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L940-SKO1-0min-rep1/L940-SKO1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L940-SKO1-0min-rep1/L940-SKO1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L940-SKO1-0min-rep1/L940-SKO1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L940-SKO1-0min-rep1/L940-SKO1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L940-SKO1-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L941-CHA4-0min-rep1/L941-CHA4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L941-CHA4-0min-rep1/L941-CHA4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L941-CHA4-0min-rep1/L941-CHA4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L941-CHA4-0min-rep1/L941-CHA4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L941-CHA4-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L942-PHO2-0min-rep1/L942-PHO2-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L942-PHO2-0min-rep1/L942-PHO2-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L942-PHO2-0min-rep1/L942-PHO2-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L942-PHO2-0min-rep1/L942-PHO2-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L942-PHO2-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L943-ROX1-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L944-HOT1-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L945-YAP5-0min-rep1/L945-YAP5-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L945-YAP5-0min-rep1/L945-YAP5-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L945-YAP5-0min-rep1/L945-YAP5-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L945-YAP5-0min-rep1/L945-YAP5-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L945-YAP5-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L946-GAT4-0min-rep1/L946-GAT4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L946-GAT4-0min-rep1/L946-GAT4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L946-GAT4-0min-rep1/L946-GAT4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L946-GAT4-0min-rep1/L946-GAT4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L946-GAT4-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L947-SKN7-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L948-MSN4-0min-rep1/L948-MSN4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L948-MSN4-0min-rep1/L948-MSN4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L948-MSN4-0min-rep1/L948-MSN4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L948-MSN4-0min-rep1/L948-MSN4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L948-MSN4-0min-rep1.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L973-HOT1-0min-rep2/L973-HOT1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L973-HOT1-0min-rep2/L973-HOT1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L973-HOT1-0min-rep2/L973-HOT1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L973-HOT1-0min-rep2/L973-HOT1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L973-HOT1-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L974-ROX1-0min-rep2/L974-ROX1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L974-ROX1-0min-rep2/L974-ROX1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L974-ROX1-0min-rep2/L974-ROX1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L974-ROX1-0min-rep2/L974-ROX1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L974-ROX1-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L975-PHO2-0min-rep2/L975-PHO2-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L975-PHO2-0min-rep2/L975-PHO2-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L975-PHO2-0min-rep2/L975-PHO2-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L975-PHO2-0min-rep2/L975-PHO2-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L975-PHO2-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L976-CHA4-0min-rep2/L976-CHA4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L976-CHA4-0min-rep2/L976-CHA4-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L976-CHA4-0min-rep2/L976-CHA4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L976-CHA4-0min-rep2/L976-CHA4-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L976-CHA4-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L977-GAT4-0min-rep2/L977-GAT4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L977-GAT4-0min-rep2/L977-GAT4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L977-GAT4-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L978-YAP5-0min-rep2/L978-YAP5-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L978-YAP5-0min-rep2/L978-YAP5-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L978-YAP5-0min-rep2/L978-YAP5-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L978-YAP5-0min-rep2/L978-YAP5-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L978-YAP5-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L979-MSN2-0min-rep2/L979-MSN2-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L979-MSN2-0min-rep2/L979-MSN2-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L979-MSN2-0min-rep2/L979-MSN2-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L979-MSN2-0min-rep2/L979-MSN2-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L979-MSN2-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L980-BDF1-0min-rep2/L980-BDF1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L980-BDF1-0min-rep2/L980-BDF1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L980-BDF1-0min-rep2/L980-BDF1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L980-BDF1-0min-rep2/L980-BDF1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L980-BDF1-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L981-SFP1-0min-rep2/L981-SFP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L981-SFP1-0min-rep2/L981-SFP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L981-SFP1-0min-rep2/L981-SFP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L981-SFP1-0min-rep2/L981-SFP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L981-SFP1-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L982-SKN7-0min-rep2/L982-SKN7-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L982-SKN7-0min-rep2/L982-SKN7-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L982-SKN7-0min-rep2/L982-SKN7-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L982-SKN7-0min-rep2/L982-SKN7-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L982-SKN7-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L983-PDR3-0min-rep2/L983-PDR3-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L983-PDR3-0min-rep2/L983-PDR3-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L983-PDR3-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L984-HOG1-0min-rep2/L984-HOG1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L984-HOG1-0min-rep2/L984-HOG1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L984-HOG1-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L985-YAP3-0min-rep2/L985-YAP3-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L985-YAP3-0min-rep2/L985-YAP3-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L985-YAP3-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L986-MSN1-0min-rep2/L986-MSN1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L986-MSN1-0min-rep2/L986-MSN1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L986-MSN1-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L987-MSN4-0min-rep2/L987-MSN4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L987-MSN4-0min-rep2/L987-MSN4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L987-MSN4-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L988-YAP6-0min-rep2/L988-YAP6-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L988-YAP6-0min-rep2/L988-YAP6-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L988-YAP6-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L989-YAP1-0min-rep2/L989-YAP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L989-YAP1-0min-rep2/L989-YAP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L989-YAP1-0min-rep2/L989-YAP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L989-YAP1-0min-rep2/L989-YAP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L989-YAP1-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L990-SMP1-0min-rep2/L990-SMP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L990-SMP1-0min-rep2/L990-SMP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L990-SMP1-0min-rep2/L990-SMP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L990-SMP1-0min-rep2/L990-SMP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L990-SMP1-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L991-ARR1-0min-rep2/L991-ARR1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L991-ARR1-0min-rep2/L991-ARR1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L991-ARR1-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L992-UME6-0min-rep2/L992-UME6-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L992-UME6-0min-rep2/L992-UME6-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L992-UME6-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L993-PHO4-0min-rep2/L993-PHO4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L993-PHO4-0min-rep2/L993-PHO4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L993-PHO4-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L994-SKO1-0min-rep2/L994-SKO1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L994-SKO1-0min-rep2/L994-SKO1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L994-SKO1-0min-rep2/L994-SKO1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L994-SKO1-0min-rep2/L994-SKO1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L994-SKO1-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L995-YAP7-0min-rep2/L995-YAP7-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L995-YAP7-0min-rep2/L995-YAP7-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L995-YAP7-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L996-GAT1-0min-rep2/L996-GAT1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L996-GAT1-0min-rep2/L996-GAT1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 20 20 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L996-GAT1-0min-rep2.2x20mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1034-Training_camp_4-HOG1-0min-rep1-ajberg5/L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1034-Training_camp_4-HOG1-0min-rep1-ajberg5/L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1035-Training_camp_5-YAP1-0min-rep2-annashch/L1035-Training_camp_5-YAP1-0min-rep2-annashch.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1035-Training_camp_5-YAP1-0min-rep2-annashch/L1035-Training_camp_5-YAP1-0min-rep2-annashch.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1035-Training_camp_5-YAP1-0min-rep2-annashch.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1037-Training_camp_7-MSN2-0min-rep2-annlin/L1037-Training_camp_7-MSN2-0min-rep2-annlin.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1037-Training_camp_7-MSN2-0min-rep2-annlin/L1037-Training_camp_7-MSN2-0min-rep2-annlin.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1037-Training_camp_7-MSN2-0min-rep2-annlin.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1040-Training_camp_10-MSN4-0min-rep2-clin5/L1040-Training_camp_10-MSN4-0min-rep2-clin5.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1040-Training_camp_10-MSN4-0min-rep2-clin5/L1040-Training_camp_10-MSN4-0min-rep2-clin5.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1040-Training_camp_10-MSN4-0min-rep2-clin5.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1042-Training_camp_12-YAP1-0min-rep1-courtrun/L1042-Training_camp_12-YAP1-0min-rep1-courtrun.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1042-Training_camp_12-YAP1-0min-rep1-courtrun/L1042-Training_camp_12-YAP1-0min-rep1-courtrun.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1042-Training_camp_12-YAP1-0min-rep1-courtrun.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1043-Training_camp_13-MSN1-0min-rep2-cvduffy/L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1043-Training_camp_13-MSN1-0min-rep2-cvduffy/L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1045-Training_camp_15-WT-0min-rep1-genegra2/L1045-Training_camp_15-WT-0min-rep1-genegra2.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1045-Training_camp_15-WT-0min-rep1-genegra2/L1045-Training_camp_15-WT-0min-rep1-genegra2.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1045-Training_camp_15-WT-0min-rep1-genegra2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1048-Training_camp_18-SKN7-0min-rep2-jarhodes/L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1048-Training_camp_18-SKN7-0min-rep2-jarhodes/L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1050-Training_camp_20-MSN4-0min-rep1-lstrand/L1050-Training_camp_20-MSN4-0min-rep1-lstrand.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1050-Training_camp_20-MSN4-0min-rep1-lstrand/L1050-Training_camp_20-MSN4-0min-rep1-lstrand.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1050-Training_camp_20-MSN4-0min-rep1-lstrand.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1052-Training_camp_22-SKN7-0min-rep1-makena/L1052-Training_camp_22-SKN7-0min-rep1-makena.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1052-Training_camp_22-SKN7-0min-rep1-makena/L1052-Training_camp_22-SKN7-0min-rep1-makena.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1052-Training_camp_22-SKN7-0min-rep1-makena.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1055-Training_camp_26-HOG1-0min-rep2-miao1/L1055-Training_camp_26-HOG1-0min-rep2-miao1.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1055-Training_camp_26-HOG1-0min-rep2-miao1/L1055-Training_camp_26-HOG1-0min-rep2-miao1.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1055-Training_camp_26-HOG1-0min-rep2-miao1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1057-Training_camp_28-HOT1-0min-rep1-myhayes/L1057-Training_camp_28-HOT1-0min-rep1-myhayes.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1057-Training_camp_28-HOT1-0min-rep1-myhayes/L1057-Training_camp_28-HOT1-0min-rep1-myhayes.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1057-Training_camp_28-HOT1-0min-rep1-myhayes.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1058-Training_camp_29-MSN1-0min-rep1-sierrasb/L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1058-Training_camp_29-MSN1-0min-rep1-sierrasb/L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1061-Training_camp_32-HOT1-0min-rep2-soumyak/L1061-Training_camp_32-HOT1-0min-rep2-soumyak.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1061-Training_camp_32-HOT1-0min-rep2-soumyak/L1061-Training_camp_32-HOT1-0min-rep2-soumyak.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1061-Training_camp_32-HOT1-0min-rep2-soumyak.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1062-Training_camp_33-WT-0min-rep2-srstern/L1062-Training_camp_33-WT-0min-rep2-srstern.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1062-Training_camp_33-WT-0min-rep2-srstern/L1062-Training_camp_33-WT-0min-rep2-srstern.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1062-Training_camp_33-WT-0min-rep2-srstern.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1064-Training_camp_35-MSN2-0min-rep1-subkc/L1064-Training_camp_35-MSN2-0min-rep1-subkc.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1064-Training_camp_35-MSN2-0min-rep1-subkc/L1064-Training_camp_35-MSN2-0min-rep1-subkc.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1064-Training_camp_35-MSN2-0min-rep1-subkc.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1067-Training_camp_38-YAP7-0min-rep2-surag/L1067-Training_camp_38-YAP7-0min-rep2-surag.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1067-Training_camp_38-YAP7-0min-rep2-surag/L1067-Training_camp_38-YAP7-0min-rep2-surag.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1067-Training_camp_38-YAP7-0min-rep2-surag.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1068-Training_camp_39-YAP6-0min-rep2-zahoor/L1068-Training_camp_39-YAP6-0min-rep2-zahoor.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1068-Training_camp_39-YAP6-0min-rep2-zahoor/L1068-Training_camp_39-YAP6-0min-rep2-zahoor.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1068-Training_camp_39-YAP6-0min-rep2-zahoor.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L665-FUN30/L665-FUN30.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L665-FUN30/L665-FUN30.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L665-FUN30/L665-FUN30.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L665-FUN30/L665-FUN30.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L665-FUN30.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L666-MSS11/L666-MSS11.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L666-MSS11/L666-MSS11.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L666-MSS11.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L667-YAP7/L667-YAP7.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L667-YAP7/L667-YAP7.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L667-YAP7.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L668-CUP9/L668-CUP9.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L668-CUP9/L668-CUP9.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L668-CUP9/L668-CUP9.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L668-CUP9/L668-CUP9.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L668-CUP9.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L669-ARG80/L669-ARG80.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L669-ARG80/L669-ARG80.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L669-ARG80/L669-ARG80.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L669-ARG80/L669-ARG80.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L669-ARG80.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L670-ARP6/L670-ARP6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L670-ARP6/L670-ARP6.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L670-ARP6/L670-ARP6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L670-ARP6/L670-ARP6.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L670-ARP6.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L671-HAP5/L671-HAP5.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L671-HAP5/L671-HAP5.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L671-HAP5.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L672-CAT8/L672-CAT8.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L672-CAT8/L672-CAT8.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L672-CAT8.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L673-RDS2/L673-RDS2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L673-RDS2/L673-RDS2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L673-RDS2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L674-CIN5/L674-CIN5.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L674-CIN5/L674-CIN5.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L674-CIN5.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L675-RDR1/L675-RDR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L675-RDR1/L675-RDR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L675-RDR1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L676-AFT2/L676-AFT2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L676-AFT2/L676-AFT2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L676-AFT2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L677-YAP1/L677-YAP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L677-YAP1/L677-YAP1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L677-YAP1/L677-YAP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L677-YAP1/L677-YAP1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L677-YAP1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L678-IOC2/L678-IOC2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L678-IOC2/L678-IOC2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L678-IOC2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L679-MAC1/L679-MAC1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L679-MAC1/L679-MAC1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L679-MAC1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L680-RTG1/L680-RTG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L680-RTG1/L680-RTG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L680-RTG1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L681-RGM1/L681-RGM1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L681-RGM1/L681-RGM1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L681-RGM1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L682-ERT1/L682-ERT1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L682-ERT1/L682-ERT1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L682-ERT1/L682-ERT1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L682-ERT1/L682-ERT1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L682-ERT1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L683-TYE7/L683-TYE7.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L683-TYE7/L683-TYE7.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L683-TYE7.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L684-DAL82/L684-DAL82.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L684-DAL82/L684-DAL82.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L684-DAL82.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L685-TEA1/L685-TEA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L685-TEA1/L685-TEA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L685-TEA1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L686-USV1/L686-USV1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L686-USV1/L686-USV1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L686-USV1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L687-SMP1/L687-SMP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L687-SMP1/L687-SMP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L687-SMP1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L688-ABF2/L688-ABF2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L688-ABF2/L688-ABF2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L688-ABF2/L688-ABF2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L688-ABF2/L688-ABF2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L688-ABF2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L689-MBP1/L689-MBP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L689-MBP1/L689-MBP1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L689-MBP1/L689-MBP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L689-MBP1/L689-MBP1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L689-MBP1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L690-CRZ1/L690-CRZ1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L690-CRZ1/L690-CRZ1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L690-CRZ1/L690-CRZ1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L690-CRZ1/L690-CRZ1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L690-CRZ1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L691-FKH2/L691-FKH2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L691-FKH2/L691-FKH2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L691-FKH2/L691-FKH2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L691-FKH2/L691-FKH2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L691-FKH2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L692-GAT4/L692-GAT4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L692-GAT4/L692-GAT4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L692-GAT4/L692-GAT4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L692-GAT4/L692-GAT4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L692-GAT4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L693-STP4/L693-STP4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L693-STP4/L693-STP4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L693-STP4/L693-STP4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L693-STP4/L693-STP4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L693-STP4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L694-IOC3/L694-IOC3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L694-IOC3/L694-IOC3.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L694-IOC3/L694-IOC3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L694-IOC3/L694-IOC3.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L694-IOC3.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L695-NRG2/L695-NRG2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L695-NRG2/L695-NRG2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L695-NRG2/L695-NRG2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L695-NRG2/L695-NRG2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L695-NRG2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L697-CST9/L697-CST9.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L697-CST9/L697-CST9.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L697-CST9.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L698-CST6/L698-CST6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L698-CST6/L698-CST6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L698-CST6.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L699-WAR1/L699-WAR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L699-WAR1/L699-WAR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L699-WAR1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L701-DAL80/L701-DAL80.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L701-DAL80/L701-DAL80.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L701-DAL80.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L702-SIR2/L702-SIR2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L702-SIR2/L702-SIR2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L702-SIR2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L704-REC8/L704-REC8.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L704-REC8/L704-REC8.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L704-REC8.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L705-TBS1/L705-TBS1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L705-TBS1/L705-TBS1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L705-TBS1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L706-URC2/L706-URC2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L706-URC2/L706-URC2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L706-URC2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L708-HDA1/L708-HDA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L708-HDA1/L708-HDA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L708-HDA1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L710-ASG1/L710-ASG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L710-ASG1/L710-ASG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L710-ASG1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L713-YNR063W/L713-YNR063W.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L713-YNR063W/L713-YNR063W.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L713-YNR063W/L713-YNR063W.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L713-YNR063W/L713-YNR063W.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L713-YNR063W.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L716-HOG1/L716-HOG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L716-HOG1/L716-HOG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L716-HOG1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L717-DOT6/L717-DOT6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L717-DOT6/L717-DOT6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L717-DOT6.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L718-MSN1/L718-MSN1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L718-MSN1/L718-MSN1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L718-MSN1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L720-INO4/L720-INO4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L720-INO4/L720-INO4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L720-INO4/L720-INO4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L720-INO4/L720-INO4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L720-INO4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L721-BYE1/L721-BYE1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L721-BYE1/L721-BYE1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L721-BYE1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L722-LSM1/L722-LSM1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L722-LSM1/L722-LSM1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L722-LSM1/L722-LSM1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L722-LSM1/L722-LSM1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L722-LSM1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L723-YER064C/L723-YER064C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L723-YER064C/L723-YER064C.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L723-YER064C/L723-YER064C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L723-YER064C/L723-YER064C.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L723-YER064C.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L725-YFL052W/L725-YFL052W.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L725-YFL052W/L725-YFL052W.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L725-YFL052W/L725-YFL052W.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L725-YFL052W/L725-YFL052W.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L725-YFL052W.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L726-HAL9/L726-HAL9.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L726-HAL9/L726-HAL9.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L726-HAL9/L726-HAL9.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L726-HAL9/L726-HAL9.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L726-HAL9.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L727-RPH1/L727-RPH1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L727-RPH1/L727-RPH1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L727-RPH1/L727-RPH1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L727-RPH1/L727-RPH1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L727-RPH1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L730-GAT1/L730-GAT1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L730-GAT1/L730-GAT1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L730-GAT1/L730-GAT1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L730-GAT1/L730-GAT1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L730-GAT1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L732-YER130C/L732-YER130C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L732-YER130C/L732-YER130C.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L732-YER130C/L732-YER130C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L732-YER130C/L732-YER130C.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L732-YER130C.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L733-RTG3/L733-RTG3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L733-RTG3/L733-RTG3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L733-RTG3.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L734-SWI4/L734-SWI4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L734-SWI4/L734-SWI4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L734-SWI4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L735-RPN4/L735-RPN4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L735-RPN4/L735-RPN4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L735-RPN4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L736-SPO11/L736-SPO11.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L736-SPO11/L736-SPO11.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L736-SPO11.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L737-STB5/L737-STB5.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L737-STB5/L737-STB5.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L737-STB5.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L738-NDT80/L738-NDT80.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L738-NDT80/L738-NDT80.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L738-NDT80.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L739-GIS1/L739-GIS1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L739-GIS1/L739-GIS1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L739-GIS1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L740-LEU3/L740-LEU3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L740-LEU3/L740-LEU3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L740-LEU3.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L741-YAP3/L741-YAP3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L741-YAP3/L741-YAP3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L741-YAP3.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L742-NRG1/L742-NRG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L742-NRG1/L742-NRG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L742-NRG1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L743-MSN4/L743-MSN4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L743-MSN4/L743-MSN4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L743-MSN4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L744-ASH1/L744-ASH1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L744-ASH1/L744-ASH1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L744-ASH1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L745-HAP4/L745-HAP4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L745-HAP4/L745-HAP4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L745-HAP4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L746-HPC2/L746-HPC2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L746-HPC2/L746-HPC2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L746-HPC2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L747-TOS8/L747-TOS8.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L747-TOS8/L747-TOS8.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L747-TOS8.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L748-HOT1/L748-HOT1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L748-HOT1/L748-HOT1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L748-HOT1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L749-KAR4/L749-KAR4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L749-KAR4/L749-KAR4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L749-KAR4/L749-KAR4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L749-KAR4/L749-KAR4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L749-KAR4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L750-AZF1/L750-AZF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L750-AZF1/L750-AZF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L750-AZF1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L751-ELG1/L751-ELG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L751-ELG1/L751-ELG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L751-ELG1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L752-YGR067C/L752-YGR067C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L752-YGR067C/L752-YGR067C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L752-YGR067C.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L753-unknown/L753-unknown.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L753-unknown/L753-unknown.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L753-unknown.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L754-LYS14/L754-LYS14.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L754-LYS14/L754-LYS14.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L754-LYS14.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L755-HIR3/L755-HIR3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L755-HIR3/L755-HIR3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L755-HIR3.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L756-STB4/L756-STB4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L756-STB4/L756-STB4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L756-STB4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L757-KTI12/L757-KTI12.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L757-KTI12/L757-KTI12.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L757-KTI12.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L758-SKN7/L758-SKN7.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L758-SKN7/L758-SKN7.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L758-SKN7.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L759-RME1/L759-RME1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L759-RME1/L759-RME1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L759-RME1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L760-ISW1/L760-ISW1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L760-ISW1/L760-ISW1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L760-ISW1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L761-FZF1/L761-FZF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L761-FZF1/L761-FZF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L761-FZF1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L762-SIP4/L762-SIP4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L762-SIP4/L762-SIP4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L762-SIP4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L763-PUT3/L763-PUT3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L763-PUT3/L763-PUT3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L763-PUT3.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L764-STP2/L764-STP2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L764-STP2/L764-STP2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L764-STP2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L765-GZF3/L765-GZF3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L765-GZF3/L765-GZF3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L765-GZF3.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L766-BAS1/L766-BAS1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L766-BAS1/L766-BAS1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L766-BAS1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L767-SUT2/L767-SUT2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L767-SUT2/L767-SUT2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L767-SUT2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L768-ROX1/L768-ROX1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L768-ROX1/L768-ROX1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L768-ROX1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L769-LIF1/L769-LIF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L769-LIF1/L769-LIF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L769-LIF1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L770-THO1/L770-THO1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L770-THO1/L770-THO1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L770-THO1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L771-HDA2/L771-HDA2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L771-HDA2/L771-HDA2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L771-HDA2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L772-NUP170/L772-NUP170.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L772-NUP170/L772-NUP170.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L772-NUP170.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L773-YPR015C/L773-YPR015C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L773-YPR015C/L773-YPR015C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L773-YPR015C.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L774-SUB1/L774-SUB1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L774-SUB1/L774-SUB1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L774-SUB1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L775-IME1/L775-IME1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L775-IME1/L775-IME1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L775-IME1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L776-HIR1/L776-HIR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L776-HIR1/L776-HIR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L776-HIR1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L777-MET32/L777-MET32.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L777-MET32/L777-MET32.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L777-MET32.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L778-RLM1/L778-RLM1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L778-RLM1/L778-RLM1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L778-RLM1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L779-YTA7/L779-YTA7.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L779-YTA7/L779-YTA7.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L779-YTA7.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L780-HIR2/L780-HIR2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L780-HIR2/L780-HIR2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L780-HIR2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L781-ZAP1/L781-ZAP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L781-ZAP1/L781-ZAP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L781-ZAP1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L782-RDS1/L782-RDS1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L782-RDS1/L782-RDS1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L782-RDS1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L783-BDF1/L783-BDF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L783-BDF1/L783-BDF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L783-BDF1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L784-HDA3/L784-HDA3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L784-HDA3/L784-HDA3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L784-HDA3.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L785-CAD1/L785-CAD1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L785-CAD1/L785-CAD1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L785-CAD1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L786-SIR4/L786-SIR4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L786-SIR4/L786-SIR4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L786-SIR4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L787-REF2/L787-REF2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L787-REF2/L787-REF2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L787-REF2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L788-MET31/L788-MET31.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L788-MET31/L788-MET31.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L788-MET31.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L789-ARO80/L789-ARO80.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L789-ARO80/L789-ARO80.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L789-ARO80.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L790-RSF2/L790-RSF2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L790-RSF2/L790-RSF2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L790-RSF2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L791-CTF4/L791-CTF4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L791-CTF4/L791-CTF4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L791-CTF4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L792-CDC73/L792-CDC73.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L792-CDC73/L792-CDC73.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L792-CDC73.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L793-OAF1/L793-OAF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L793-OAF1/L793-OAF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L793-OAF1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L794-UPC2/L794-UPC2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L794-UPC2/L794-UPC2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L794-UPC2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L795-MIG3/L795-MIG3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L795-MIG3/L795-MIG3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L795-MIG3.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L796-UME6/L796-UME6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L796-UME6/L796-UME6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L796-UME6.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L797-REI1/L797-REI1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L797-REI1/L797-REI1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L797-REI1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L798-YLR278C/L798-YLR278C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L798-YLR278C/L798-YLR278C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L798-YLR278C.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L799-SFP1/L799-SFP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L799-SFP1/L799-SFP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L799-SFP1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L800-ECM23/L800-ECM23.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L800-ECM23/L800-ECM23.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L800-ECM23.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L801-VHR1/L801-VHR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L801-VHR1/L801-VHR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L801-VHR1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L802-DHH1/L802-DHH1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L802-DHH1/L802-DHH1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L802-DHH1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L803-YAP6/L803-YAP6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L803-YAP6/L803-YAP6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L803-YAP6.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L804-GCN4/L804-GCN4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L804-GCN4/L804-GCN4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L804-GCN4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L805-PDR1/L805-PDR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L805-PDR1/L805-PDR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L805-PDR1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L806-MIG2/L806-MIG2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L806-MIG2/L806-MIG2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L806-MIG2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L807-ADR1/L807-ADR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L807-ADR1/L807-ADR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L807-ADR1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L808-YPR022C/L808-YPR022C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L808-YPR022C/L808-YPR022C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L808-YPR022C.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L809-HAA1/L809-HAA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L809-HAA1/L809-HAA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L809-HAA1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L810-ARR1/L810-ARR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L810-ARR1/L810-ARR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L810-ARR1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L811-YPR013C/L811-YPR013C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L811-YPR013C/L811-YPR013C.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L811-YPR013C/L811-YPR013C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L811-YPR013C/L811-YPR013C.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L811-YPR013C.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L812-RGT1/L812-RGT1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L812-RGT1/L812-RGT1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L812-RGT1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L813-RFX1/L813-RFX1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L813-RFX1/L813-RFX1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L813-RFX1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L814-IXR1/L814-IXR1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L814-IXR1/L814-IXR1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L814-IXR1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L815-PDR8/L815-PDR8.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L815-PDR8/L815-PDR8.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L815-PDR8.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L816-ECM22/L816-ECM22.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L816-ECM22/L816-ECM22.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L816-ECM22.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L817-XRN1/L817-XRN1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L817-XRN1/L817-XRN1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L817-XRN1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L818-YRR1/L818-YRR1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L818-YRR1/L818-YRR1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L818-YRR1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L819-MSN2/L819-MSN2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L819-MSN2/L819-MSN2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L819-MSN2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L820-YPR196W/L820-YPR196W.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L820-YPR196W/L820-YPR196W.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L820-YPR196W.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L821-DAL81/L821-DAL81.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L821-DAL81/L821-DAL81.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L821-DAL81.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L822-HAT1/L822-HAT1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L822-HAT1/L822-HAT1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L822-HAT1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L823-PAF1/L823-PAF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L823-PAF1/L823-PAF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L823-PAF1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L824-NHP10/L824-NHP10.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L824-NHP10/L824-NHP10.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L824-NHP10.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L825-SPP1/L825-SPP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L825-SPP1/L825-SPP1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L825-SPP1/L825-SPP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L825-SPP1/L825-SPP1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L825-SPP1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L826-SFL1/L826-SFL1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L826-SFL1/L826-SFL1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L826-SFL1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L827-STP3/L827-STP3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L827-STP3/L827-STP3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L827-STP3.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L828-YRM1/L828-YRM1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L828-YRM1/L828-YRM1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L828-YRM1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L829-ISW2/L829-ISW2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L829-ISW2/L829-ISW2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L829-ISW2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L830-HTZ1/L830-HTZ1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L830-HTZ1/L830-HTZ1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L830-HTZ1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L831-PHD1/L831-PHD1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L831-PHD1/L831-PHD1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L831-PHD1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L832-SWI5/L832-SWI5.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L832-SWI5/L832-SWI5.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L832-SWI5/L832-SWI5.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L832-SWI5/L832-SWI5.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L832-SWI5.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L833-ACA1/L833-ACA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L833-ACA1/L833-ACA1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L833-ACA1/L833-ACA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L833-ACA1/L833-ACA1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L833-ACA1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L834-INO2/L834-INO2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L834-INO2/L834-INO2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L834-INO2/L834-INO2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L834-INO2/L834-INO2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L834-INO2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L835-PHO4/L835-PHO4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L835-PHO4/L835-PHO4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L835-PHO4/L835-PHO4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L835-PHO4/L835-PHO4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L835-PHO4.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L836-MGA1/L836-MGA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L836-MGA1/L836-MGA1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L836-MGA1/L836-MGA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L836-MGA1/L836-MGA1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L836-MGA1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L837-MIG1/L837-MIG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L837-MIG1/L837-MIG1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L837-MIG1/L837-MIG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L837-MIG1/L837-MIG1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L837-MIG1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L838-HAP3/L838-HAP3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L838-HAP3/L838-HAP3.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L838-HAP3/L838-HAP3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L838-HAP3/L838-HAP3.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L838-HAP3.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L839-YHR177W/L839-YHR177W.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L839-YHR177W/L839-YHR177W.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L839-YHR177W/L839-YHR177W.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L839-YHR177W/L839-YHR177W.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L839-YHR177W.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L847-GLN3/L847-GLN3.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L847-GLN3/L847-GLN3.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L847-GLN3.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L848-TOD6/L848-TOD6.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L848-TOD6/L848-TOD6.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L848-TOD6.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L925-MSN2-0min-rep1/L925-MSN2-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L925-MSN2-0min-rep1/L925-MSN2-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L925-MSN2-0min-rep1/L925-MSN2-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L925-MSN2-0min-rep1/L925-MSN2-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L925-MSN2-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L927-MSN1-0min-rep1/L927-MSN1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L927-MSN1-0min-rep1/L927-MSN1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L927-MSN1-0min-rep1/L927-MSN1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L927-MSN1-0min-rep1/L927-MSN1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L927-MSN1-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L928-HOG1-0min-rep1/L928-HOG1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L928-HOG1-0min-rep1/L928-HOG1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L928-HOG1-0min-rep1/L928-HOG1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L928-HOG1-0min-rep1/L928-HOG1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L928-HOG1-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L929-BDF1-0min-rep1/L929-BDF1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L929-BDF1-0min-rep1/L929-BDF1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L929-BDF1-0min-rep1/L929-BDF1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L929-BDF1-0min-rep1/L929-BDF1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L929-BDF1-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L930-YAP7-0min-rep1/L930-YAP7-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L930-YAP7-0min-rep1/L930-YAP7-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L930-YAP7-0min-rep1/L930-YAP7-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L930-YAP7-0min-rep1/L930-YAP7-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L930-YAP7-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L931-UME6-0min-rep1/L931-UME6-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L931-UME6-0min-rep1/L931-UME6-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L931-UME6-0min-rep1/L931-UME6-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L931-UME6-0min-rep1/L931-UME6-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L931-UME6-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L932-SMP1-0min-rep1/L932-SMP1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L932-SMP1-0min-rep1/L932-SMP1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L932-SMP1-0min-rep1/L932-SMP1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L932-SMP1-0min-rep1/L932-SMP1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L932-SMP1-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L933-YAP1-0min-rep1/L933-YAP1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L933-YAP1-0min-rep1/L933-YAP1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L933-YAP1-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L934-YAP3-0min-rep1/L934-YAP3-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L934-YAP3-0min-rep1/L934-YAP3-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L934-YAP3-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L935-ARR1-0min-rep1/L935-ARR1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L935-ARR1-0min-rep1/L935-ARR1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L935-ARR1-0min-rep1/L935-ARR1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L935-ARR1-0min-rep1/L935-ARR1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L935-ARR1-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L936-PHO4-0min-rep1/L936-PHO4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L936-PHO4-0min-rep1/L936-PHO4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L936-PHO4-0min-rep1/L936-PHO4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L936-PHO4-0min-rep1/L936-PHO4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L936-PHO4-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L937-YAP6-0min-rep1/L937-YAP6-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L937-YAP6-0min-rep1/L937-YAP6-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L937-YAP6-0min-rep1/L937-YAP6-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L937-YAP6-0min-rep1/L937-YAP6-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L937-YAP6-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L938-PDR3-0min-rep1/L938-PDR3-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L938-PDR3-0min-rep1/L938-PDR3-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L938-PDR3-0min-rep1/L938-PDR3-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L938-PDR3-0min-rep1/L938-PDR3-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L938-PDR3-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L939-GAT1-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L940-SKO1-0min-rep1/L940-SKO1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L940-SKO1-0min-rep1/L940-SKO1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L940-SKO1-0min-rep1/L940-SKO1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L940-SKO1-0min-rep1/L940-SKO1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L940-SKO1-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L941-CHA4-0min-rep1/L941-CHA4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L941-CHA4-0min-rep1/L941-CHA4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L941-CHA4-0min-rep1/L941-CHA4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L941-CHA4-0min-rep1/L941-CHA4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L941-CHA4-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L942-PHO2-0min-rep1/L942-PHO2-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L942-PHO2-0min-rep1/L942-PHO2-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L942-PHO2-0min-rep1/L942-PHO2-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L942-PHO2-0min-rep1/L942-PHO2-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L942-PHO2-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L943-ROX1-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L944-HOT1-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L945-YAP5-0min-rep1/L945-YAP5-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L945-YAP5-0min-rep1/L945-YAP5-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L945-YAP5-0min-rep1/L945-YAP5-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L945-YAP5-0min-rep1/L945-YAP5-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L945-YAP5-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L946-GAT4-0min-rep1/L946-GAT4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L946-GAT4-0min-rep1/L946-GAT4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L946-GAT4-0min-rep1/L946-GAT4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L946-GAT4-0min-rep1/L946-GAT4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L946-GAT4-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L947-SKN7-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L948-MSN4-0min-rep1/L948-MSN4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L948-MSN4-0min-rep1/L948-MSN4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L948-MSN4-0min-rep1/L948-MSN4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L948-MSN4-0min-rep1/L948-MSN4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L948-MSN4-0min-rep1.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L973-HOT1-0min-rep2/L973-HOT1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L973-HOT1-0min-rep2/L973-HOT1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L973-HOT1-0min-rep2/L973-HOT1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L973-HOT1-0min-rep2/L973-HOT1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L973-HOT1-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L974-ROX1-0min-rep2/L974-ROX1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L974-ROX1-0min-rep2/L974-ROX1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L974-ROX1-0min-rep2/L974-ROX1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L974-ROX1-0min-rep2/L974-ROX1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L974-ROX1-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L975-PHO2-0min-rep2/L975-PHO2-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L975-PHO2-0min-rep2/L975-PHO2-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L975-PHO2-0min-rep2/L975-PHO2-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L975-PHO2-0min-rep2/L975-PHO2-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L975-PHO2-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L976-CHA4-0min-rep2/L976-CHA4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L976-CHA4-0min-rep2/L976-CHA4-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L976-CHA4-0min-rep2/L976-CHA4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L976-CHA4-0min-rep2/L976-CHA4-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L976-CHA4-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L977-GAT4-0min-rep2/L977-GAT4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L977-GAT4-0min-rep2/L977-GAT4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L977-GAT4-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L978-YAP5-0min-rep2/L978-YAP5-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L978-YAP5-0min-rep2/L978-YAP5-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L978-YAP5-0min-rep2/L978-YAP5-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L978-YAP5-0min-rep2/L978-YAP5-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L978-YAP5-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L979-MSN2-0min-rep2/L979-MSN2-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L979-MSN2-0min-rep2/L979-MSN2-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L979-MSN2-0min-rep2/L979-MSN2-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L979-MSN2-0min-rep2/L979-MSN2-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L979-MSN2-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L980-BDF1-0min-rep2/L980-BDF1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L980-BDF1-0min-rep2/L980-BDF1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L980-BDF1-0min-rep2/L980-BDF1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L980-BDF1-0min-rep2/L980-BDF1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L980-BDF1-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L981-SFP1-0min-rep2/L981-SFP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L981-SFP1-0min-rep2/L981-SFP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L981-SFP1-0min-rep2/L981-SFP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L981-SFP1-0min-rep2/L981-SFP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L981-SFP1-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L982-SKN7-0min-rep2/L982-SKN7-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L982-SKN7-0min-rep2/L982-SKN7-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L982-SKN7-0min-rep2/L982-SKN7-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L982-SKN7-0min-rep2/L982-SKN7-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L982-SKN7-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L983-PDR3-0min-rep2/L983-PDR3-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L983-PDR3-0min-rep2/L983-PDR3-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L983-PDR3-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L984-HOG1-0min-rep2/L984-HOG1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L984-HOG1-0min-rep2/L984-HOG1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L984-HOG1-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L985-YAP3-0min-rep2/L985-YAP3-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L985-YAP3-0min-rep2/L985-YAP3-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L985-YAP3-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L986-MSN1-0min-rep2/L986-MSN1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L986-MSN1-0min-rep2/L986-MSN1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L986-MSN1-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L987-MSN4-0min-rep2/L987-MSN4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L987-MSN4-0min-rep2/L987-MSN4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L987-MSN4-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L988-YAP6-0min-rep2/L988-YAP6-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L988-YAP6-0min-rep2/L988-YAP6-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L988-YAP6-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L989-YAP1-0min-rep2/L989-YAP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L989-YAP1-0min-rep2/L989-YAP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L989-YAP1-0min-rep2/L989-YAP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L989-YAP1-0min-rep2/L989-YAP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L989-YAP1-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L990-SMP1-0min-rep2/L990-SMP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L990-SMP1-0min-rep2/L990-SMP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L990-SMP1-0min-rep2/L990-SMP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L990-SMP1-0min-rep2/L990-SMP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L990-SMP1-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L991-ARR1-0min-rep2/L991-ARR1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L991-ARR1-0min-rep2/L991-ARR1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L991-ARR1-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L992-UME6-0min-rep2/L992-UME6-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L992-UME6-0min-rep2/L992-UME6-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L992-UME6-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L993-PHO4-0min-rep2/L993-PHO4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L993-PHO4-0min-rep2/L993-PHO4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L993-PHO4-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L994-SKO1-0min-rep2/L994-SKO1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L994-SKO1-0min-rep2/L994-SKO1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L994-SKO1-0min-rep2/L994-SKO1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L994-SKO1-0min-rep2/L994-SKO1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L994-SKO1-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L995-YAP7-0min-rep2/L995-YAP7-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L995-YAP7-0min-rep2/L995-YAP7-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L995-YAP7-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L996-GAT1-0min-rep2/L996-GAT1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L996-GAT1-0min-rep2/L996-GAT1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 15 15 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L996-GAT1-0min-rep2.2x15mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1034-Training_camp_4-HOG1-0min-rep1-ajberg5/L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1034-Training_camp_4-HOG1-0min-rep1-ajberg5/L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1035-Training_camp_5-YAP1-0min-rep2-annashch/L1035-Training_camp_5-YAP1-0min-rep2-annashch.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1035-Training_camp_5-YAP1-0min-rep2-annashch/L1035-Training_camp_5-YAP1-0min-rep2-annashch.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1035-Training_camp_5-YAP1-0min-rep2-annashch.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1037-Training_camp_7-MSN2-0min-rep2-annlin/L1037-Training_camp_7-MSN2-0min-rep2-annlin.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1037-Training_camp_7-MSN2-0min-rep2-annlin/L1037-Training_camp_7-MSN2-0min-rep2-annlin.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1037-Training_camp_7-MSN2-0min-rep2-annlin.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1040-Training_camp_10-MSN4-0min-rep2-clin5/L1040-Training_camp_10-MSN4-0min-rep2-clin5.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1040-Training_camp_10-MSN4-0min-rep2-clin5/L1040-Training_camp_10-MSN4-0min-rep2-clin5.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1040-Training_camp_10-MSN4-0min-rep2-clin5.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1042-Training_camp_12-YAP1-0min-rep1-courtrun/L1042-Training_camp_12-YAP1-0min-rep1-courtrun.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1042-Training_camp_12-YAP1-0min-rep1-courtrun/L1042-Training_camp_12-YAP1-0min-rep1-courtrun.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1042-Training_camp_12-YAP1-0min-rep1-courtrun.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1043-Training_camp_13-MSN1-0min-rep2-cvduffy/L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1043-Training_camp_13-MSN1-0min-rep2-cvduffy/L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1045-Training_camp_15-WT-0min-rep1-genegra2/L1045-Training_camp_15-WT-0min-rep1-genegra2.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1045-Training_camp_15-WT-0min-rep1-genegra2/L1045-Training_camp_15-WT-0min-rep1-genegra2.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1045-Training_camp_15-WT-0min-rep1-genegra2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1048-Training_camp_18-SKN7-0min-rep2-jarhodes/L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1048-Training_camp_18-SKN7-0min-rep2-jarhodes/L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1050-Training_camp_20-MSN4-0min-rep1-lstrand/L1050-Training_camp_20-MSN4-0min-rep1-lstrand.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1050-Training_camp_20-MSN4-0min-rep1-lstrand/L1050-Training_camp_20-MSN4-0min-rep1-lstrand.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1050-Training_camp_20-MSN4-0min-rep1-lstrand.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1052-Training_camp_22-SKN7-0min-rep1-makena/L1052-Training_camp_22-SKN7-0min-rep1-makena.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1052-Training_camp_22-SKN7-0min-rep1-makena/L1052-Training_camp_22-SKN7-0min-rep1-makena.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1052-Training_camp_22-SKN7-0min-rep1-makena.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1055-Training_camp_26-HOG1-0min-rep2-miao1/L1055-Training_camp_26-HOG1-0min-rep2-miao1.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1055-Training_camp_26-HOG1-0min-rep2-miao1/L1055-Training_camp_26-HOG1-0min-rep2-miao1.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1055-Training_camp_26-HOG1-0min-rep2-miao1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1057-Training_camp_28-HOT1-0min-rep1-myhayes/L1057-Training_camp_28-HOT1-0min-rep1-myhayes.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1057-Training_camp_28-HOT1-0min-rep1-myhayes/L1057-Training_camp_28-HOT1-0min-rep1-myhayes.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1057-Training_camp_28-HOT1-0min-rep1-myhayes.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1058-Training_camp_29-MSN1-0min-rep1-sierrasb/L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1058-Training_camp_29-MSN1-0min-rep1-sierrasb/L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1061-Training_camp_32-HOT1-0min-rep2-soumyak/L1061-Training_camp_32-HOT1-0min-rep2-soumyak.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1061-Training_camp_32-HOT1-0min-rep2-soumyak/L1061-Training_camp_32-HOT1-0min-rep2-soumyak.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1061-Training_camp_32-HOT1-0min-rep2-soumyak.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1062-Training_camp_33-WT-0min-rep2-srstern/L1062-Training_camp_33-WT-0min-rep2-srstern.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1062-Training_camp_33-WT-0min-rep2-srstern/L1062-Training_camp_33-WT-0min-rep2-srstern.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1062-Training_camp_33-WT-0min-rep2-srstern.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1064-Training_camp_35-MSN2-0min-rep1-subkc/L1064-Training_camp_35-MSN2-0min-rep1-subkc.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1064-Training_camp_35-MSN2-0min-rep1-subkc/L1064-Training_camp_35-MSN2-0min-rep1-subkc.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1064-Training_camp_35-MSN2-0min-rep1-subkc.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1067-Training_camp_38-YAP7-0min-rep2-surag/L1067-Training_camp_38-YAP7-0min-rep2-surag.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1067-Training_camp_38-YAP7-0min-rep2-surag/L1067-Training_camp_38-YAP7-0min-rep2-surag.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1067-Training_camp_38-YAP7-0min-rep2-surag.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1068-Training_camp_39-YAP6-0min-rep2-zahoor/L1068-Training_camp_39-YAP6-0min-rep2-zahoor.190916_NB551514_0277_AHV3LKBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L1068-Training_camp_39-YAP6-0min-rep2-zahoor/L1068-Training_camp_39-YAP6-0min-rep2-zahoor.190916_NB551514_0277_AHV3LKBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1068-Training_camp_39-YAP6-0min-rep2-zahoor.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L665-FUN30/L665-FUN30.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L665-FUN30/L665-FUN30.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L665-FUN30/L665-FUN30.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L665-FUN30/L665-FUN30.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L665-FUN30.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L666-MSS11/L666-MSS11.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L666-MSS11/L666-MSS11.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L666-MSS11.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L667-YAP7/L667-YAP7.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L667-YAP7/L667-YAP7.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L667-YAP7.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L668-CUP9/L668-CUP9.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L668-CUP9/L668-CUP9.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L668-CUP9/L668-CUP9.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L668-CUP9/L668-CUP9.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L668-CUP9.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L669-ARG80/L669-ARG80.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L669-ARG80/L669-ARG80.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L669-ARG80/L669-ARG80.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L669-ARG80/L669-ARG80.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L669-ARG80.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L670-ARP6/L670-ARP6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L670-ARP6/L670-ARP6.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L670-ARP6/L670-ARP6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L670-ARP6/L670-ARP6.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L670-ARP6.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L671-HAP5/L671-HAP5.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L671-HAP5/L671-HAP5.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L671-HAP5.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L672-CAT8/L672-CAT8.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L672-CAT8/L672-CAT8.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L672-CAT8.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L673-RDS2/L673-RDS2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L673-RDS2/L673-RDS2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L673-RDS2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L674-CIN5/L674-CIN5.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L674-CIN5/L674-CIN5.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L674-CIN5.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L675-RDR1/L675-RDR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L675-RDR1/L675-RDR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L675-RDR1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L676-AFT2/L676-AFT2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L676-AFT2/L676-AFT2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L676-AFT2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L677-YAP1/L677-YAP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L677-YAP1/L677-YAP1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L677-YAP1/L677-YAP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L677-YAP1/L677-YAP1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L677-YAP1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L678-IOC2/L678-IOC2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L678-IOC2/L678-IOC2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L678-IOC2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L679-MAC1/L679-MAC1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L679-MAC1/L679-MAC1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L679-MAC1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L680-RTG1/L680-RTG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L680-RTG1/L680-RTG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L680-RTG1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L681-RGM1/L681-RGM1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L681-RGM1/L681-RGM1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L681-RGM1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L682-ERT1/L682-ERT1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L682-ERT1/L682-ERT1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L682-ERT1/L682-ERT1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L682-ERT1/L682-ERT1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L682-ERT1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L683-TYE7/L683-TYE7.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L683-TYE7/L683-TYE7.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L683-TYE7.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L684-DAL82/L684-DAL82.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L684-DAL82/L684-DAL82.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L684-DAL82.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L685-TEA1/L685-TEA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L685-TEA1/L685-TEA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L685-TEA1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L686-USV1/L686-USV1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L686-USV1/L686-USV1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L686-USV1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L687-SMP1/L687-SMP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L687-SMP1/L687-SMP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L687-SMP1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L688-ABF2/L688-ABF2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L688-ABF2/L688-ABF2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L688-ABF2/L688-ABF2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L688-ABF2/L688-ABF2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L688-ABF2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L689-MBP1/L689-MBP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L689-MBP1/L689-MBP1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L689-MBP1/L689-MBP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L689-MBP1/L689-MBP1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L689-MBP1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L690-CRZ1/L690-CRZ1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L690-CRZ1/L690-CRZ1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L690-CRZ1/L690-CRZ1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L690-CRZ1/L690-CRZ1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L690-CRZ1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L691-FKH2/L691-FKH2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L691-FKH2/L691-FKH2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L691-FKH2/L691-FKH2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L691-FKH2/L691-FKH2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L691-FKH2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L692-GAT4/L692-GAT4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L692-GAT4/L692-GAT4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L692-GAT4/L692-GAT4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L692-GAT4/L692-GAT4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L692-GAT4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L693-STP4/L693-STP4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L693-STP4/L693-STP4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L693-STP4/L693-STP4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L693-STP4/L693-STP4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L693-STP4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L694-IOC3/L694-IOC3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L694-IOC3/L694-IOC3.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L694-IOC3/L694-IOC3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L694-IOC3/L694-IOC3.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L694-IOC3.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L695-NRG2/L695-NRG2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L695-NRG2/L695-NRG2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L695-NRG2/L695-NRG2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L695-NRG2/L695-NRG2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L695-NRG2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L697-CST9/L697-CST9.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L697-CST9/L697-CST9.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L697-CST9.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L698-CST6/L698-CST6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L698-CST6/L698-CST6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L698-CST6.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L699-WAR1/L699-WAR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L699-WAR1/L699-WAR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L699-WAR1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L701-DAL80/L701-DAL80.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L701-DAL80/L701-DAL80.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L701-DAL80.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L702-SIR2/L702-SIR2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L702-SIR2/L702-SIR2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L702-SIR2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L704-REC8/L704-REC8.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L704-REC8/L704-REC8.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L704-REC8.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L705-TBS1/L705-TBS1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L705-TBS1/L705-TBS1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L705-TBS1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L706-URC2/L706-URC2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L706-URC2/L706-URC2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L706-URC2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L708-HDA1/L708-HDA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L708-HDA1/L708-HDA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L708-HDA1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L710-ASG1/L710-ASG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L710-ASG1/L710-ASG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L710-ASG1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L713-YNR063W/L713-YNR063W.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L713-YNR063W/L713-YNR063W.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L713-YNR063W/L713-YNR063W.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L713-YNR063W/L713-YNR063W.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L713-YNR063W.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L716-HOG1/L716-HOG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L716-HOG1/L716-HOG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L716-HOG1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L717-DOT6/L717-DOT6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L717-DOT6/L717-DOT6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L717-DOT6.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L718-MSN1/L718-MSN1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L718-MSN1/L718-MSN1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L718-MSN1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L720-INO4/L720-INO4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L720-INO4/L720-INO4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L720-INO4/L720-INO4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L720-INO4/L720-INO4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L720-INO4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L721-BYE1/L721-BYE1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L721-BYE1/L721-BYE1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L721-BYE1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L722-LSM1/L722-LSM1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L722-LSM1/L722-LSM1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L722-LSM1/L722-LSM1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L722-LSM1/L722-LSM1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L722-LSM1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L723-YER064C/L723-YER064C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L723-YER064C/L723-YER064C.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L723-YER064C/L723-YER064C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L723-YER064C/L723-YER064C.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L723-YER064C.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L725-YFL052W/L725-YFL052W.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L725-YFL052W/L725-YFL052W.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L725-YFL052W/L725-YFL052W.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L725-YFL052W/L725-YFL052W.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L725-YFL052W.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L726-HAL9/L726-HAL9.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L726-HAL9/L726-HAL9.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L726-HAL9/L726-HAL9.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L726-HAL9/L726-HAL9.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L726-HAL9.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L727-RPH1/L727-RPH1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L727-RPH1/L727-RPH1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L727-RPH1/L727-RPH1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L727-RPH1/L727-RPH1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L727-RPH1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L730-GAT1/L730-GAT1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L730-GAT1/L730-GAT1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L730-GAT1/L730-GAT1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L730-GAT1/L730-GAT1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L730-GAT1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L732-YER130C/L732-YER130C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L732-YER130C/L732-YER130C.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L732-YER130C/L732-YER130C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L732-YER130C/L732-YER130C.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L732-YER130C.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L733-RTG3/L733-RTG3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L733-RTG3/L733-RTG3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L733-RTG3.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L734-SWI4/L734-SWI4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L734-SWI4/L734-SWI4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L734-SWI4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L735-RPN4/L735-RPN4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L735-RPN4/L735-RPN4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L735-RPN4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L736-SPO11/L736-SPO11.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L736-SPO11/L736-SPO11.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L736-SPO11.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L737-STB5/L737-STB5.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L737-STB5/L737-STB5.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L737-STB5.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L738-NDT80/L738-NDT80.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L738-NDT80/L738-NDT80.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L738-NDT80.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L739-GIS1/L739-GIS1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L739-GIS1/L739-GIS1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L739-GIS1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L740-LEU3/L740-LEU3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L740-LEU3/L740-LEU3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L740-LEU3.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L741-YAP3/L741-YAP3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L741-YAP3/L741-YAP3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L741-YAP3.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L742-NRG1/L742-NRG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L742-NRG1/L742-NRG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L742-NRG1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L743-MSN4/L743-MSN4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L743-MSN4/L743-MSN4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L743-MSN4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L744-ASH1/L744-ASH1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L744-ASH1/L744-ASH1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L744-ASH1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L745-HAP4/L745-HAP4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L745-HAP4/L745-HAP4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L745-HAP4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L746-HPC2/L746-HPC2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L746-HPC2/L746-HPC2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L746-HPC2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L747-TOS8/L747-TOS8.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L747-TOS8/L747-TOS8.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L747-TOS8.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L748-HOT1/L748-HOT1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L748-HOT1/L748-HOT1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L748-HOT1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L749-KAR4/L749-KAR4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L749-KAR4/L749-KAR4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L749-KAR4/L749-KAR4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L749-KAR4/L749-KAR4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L749-KAR4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L750-AZF1/L750-AZF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L750-AZF1/L750-AZF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L750-AZF1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L751-ELG1/L751-ELG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L751-ELG1/L751-ELG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L751-ELG1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L752-YGR067C/L752-YGR067C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L752-YGR067C/L752-YGR067C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L752-YGR067C.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L753-unknown/L753-unknown.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L753-unknown/L753-unknown.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L753-unknown.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L754-LYS14/L754-LYS14.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L754-LYS14/L754-LYS14.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L754-LYS14.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L755-HIR3/L755-HIR3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L755-HIR3/L755-HIR3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L755-HIR3.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L756-STB4/L756-STB4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L756-STB4/L756-STB4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L756-STB4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L757-KTI12/L757-KTI12.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L757-KTI12/L757-KTI12.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L757-KTI12.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L758-SKN7/L758-SKN7.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L758-SKN7/L758-SKN7.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L758-SKN7.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L759-RME1/L759-RME1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L759-RME1/L759-RME1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L759-RME1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L760-ISW1/L760-ISW1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L760-ISW1/L760-ISW1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L760-ISW1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L761-FZF1/L761-FZF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L761-FZF1/L761-FZF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L761-FZF1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L762-SIP4/L762-SIP4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L762-SIP4/L762-SIP4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L762-SIP4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L763-PUT3/L763-PUT3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L763-PUT3/L763-PUT3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L763-PUT3.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L764-STP2/L764-STP2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L764-STP2/L764-STP2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L764-STP2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L765-GZF3/L765-GZF3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L765-GZF3/L765-GZF3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L765-GZF3.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L766-BAS1/L766-BAS1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L766-BAS1/L766-BAS1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L766-BAS1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L767-SUT2/L767-SUT2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L767-SUT2/L767-SUT2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L767-SUT2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L768-ROX1/L768-ROX1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L768-ROX1/L768-ROX1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L768-ROX1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L769-LIF1/L769-LIF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L769-LIF1/L769-LIF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L769-LIF1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L770-THO1/L770-THO1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L770-THO1/L770-THO1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L770-THO1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L771-HDA2/L771-HDA2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L771-HDA2/L771-HDA2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L771-HDA2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L772-NUP170/L772-NUP170.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L772-NUP170/L772-NUP170.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L772-NUP170.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L773-YPR015C/L773-YPR015C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L773-YPR015C/L773-YPR015C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L773-YPR015C.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L774-SUB1/L774-SUB1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L774-SUB1/L774-SUB1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L774-SUB1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L775-IME1/L775-IME1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L775-IME1/L775-IME1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L775-IME1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L776-HIR1/L776-HIR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L776-HIR1/L776-HIR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L776-HIR1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L777-MET32/L777-MET32.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L777-MET32/L777-MET32.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L777-MET32.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L778-RLM1/L778-RLM1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L778-RLM1/L778-RLM1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L778-RLM1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L779-YTA7/L779-YTA7.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L779-YTA7/L779-YTA7.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L779-YTA7.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L780-HIR2/L780-HIR2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L780-HIR2/L780-HIR2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L780-HIR2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L781-ZAP1/L781-ZAP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L781-ZAP1/L781-ZAP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L781-ZAP1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L782-RDS1/L782-RDS1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L782-RDS1/L782-RDS1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L782-RDS1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L783-BDF1/L783-BDF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L783-BDF1/L783-BDF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L783-BDF1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L784-HDA3/L784-HDA3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L784-HDA3/L784-HDA3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L784-HDA3.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L785-CAD1/L785-CAD1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L785-CAD1/L785-CAD1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L785-CAD1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L786-SIR4/L786-SIR4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L786-SIR4/L786-SIR4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L786-SIR4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L787-REF2/L787-REF2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L787-REF2/L787-REF2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L787-REF2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L788-MET31/L788-MET31.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L788-MET31/L788-MET31.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L788-MET31.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L789-ARO80/L789-ARO80.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L789-ARO80/L789-ARO80.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L789-ARO80.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L790-RSF2/L790-RSF2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L790-RSF2/L790-RSF2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L790-RSF2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L791-CTF4/L791-CTF4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L791-CTF4/L791-CTF4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L791-CTF4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L792-CDC73/L792-CDC73.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L792-CDC73/L792-CDC73.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L792-CDC73.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L793-OAF1/L793-OAF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L793-OAF1/L793-OAF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L793-OAF1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L794-UPC2/L794-UPC2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L794-UPC2/L794-UPC2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L794-UPC2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L795-MIG3/L795-MIG3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L795-MIG3/L795-MIG3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L795-MIG3.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L796-UME6/L796-UME6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L796-UME6/L796-UME6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L796-UME6.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L797-REI1/L797-REI1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L797-REI1/L797-REI1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L797-REI1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L798-YLR278C/L798-YLR278C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L798-YLR278C/L798-YLR278C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L798-YLR278C.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L799-SFP1/L799-SFP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L799-SFP1/L799-SFP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L799-SFP1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L800-ECM23/L800-ECM23.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L800-ECM23/L800-ECM23.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L800-ECM23.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L801-VHR1/L801-VHR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L801-VHR1/L801-VHR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L801-VHR1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L802-DHH1/L802-DHH1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L802-DHH1/L802-DHH1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L802-DHH1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L803-YAP6/L803-YAP6.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L803-YAP6/L803-YAP6.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L803-YAP6.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L804-GCN4/L804-GCN4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L804-GCN4/L804-GCN4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L804-GCN4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L805-PDR1/L805-PDR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L805-PDR1/L805-PDR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L805-PDR1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L806-MIG2/L806-MIG2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L806-MIG2/L806-MIG2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L806-MIG2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L807-ADR1/L807-ADR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L807-ADR1/L807-ADR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L807-ADR1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L808-YPR022C/L808-YPR022C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L808-YPR022C/L808-YPR022C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L808-YPR022C.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L809-HAA1/L809-HAA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L809-HAA1/L809-HAA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L809-HAA1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L810-ARR1/L810-ARR1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L810-ARR1/L810-ARR1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L810-ARR1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L811-YPR013C/L811-YPR013C.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L811-YPR013C/L811-YPR013C.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L811-YPR013C/L811-YPR013C.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L811-YPR013C/L811-YPR013C.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L811-YPR013C.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L812-RGT1/L812-RGT1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L812-RGT1/L812-RGT1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L812-RGT1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L813-RFX1/L813-RFX1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L813-RFX1/L813-RFX1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L813-RFX1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L814-IXR1/L814-IXR1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L814-IXR1/L814-IXR1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L814-IXR1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L815-PDR8/L815-PDR8.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L815-PDR8/L815-PDR8.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L815-PDR8.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L816-ECM22/L816-ECM22.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L816-ECM22/L816-ECM22.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L816-ECM22.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L817-XRN1/L817-XRN1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L817-XRN1/L817-XRN1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L817-XRN1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L818-YRR1/L818-YRR1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L818-YRR1/L818-YRR1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L818-YRR1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L819-MSN2/L819-MSN2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L819-MSN2/L819-MSN2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L819-MSN2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L820-YPR196W/L820-YPR196W.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L820-YPR196W/L820-YPR196W.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L820-YPR196W.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L821-DAL81/L821-DAL81.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L821-DAL81/L821-DAL81.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L821-DAL81.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L822-HAT1/L822-HAT1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L822-HAT1/L822-HAT1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L822-HAT1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L823-PAF1/L823-PAF1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L823-PAF1/L823-PAF1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L823-PAF1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L824-NHP10/L824-NHP10.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L824-NHP10/L824-NHP10.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L824-NHP10.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L825-SPP1/L825-SPP1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L825-SPP1/L825-SPP1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L825-SPP1/L825-SPP1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L825-SPP1/L825-SPP1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L825-SPP1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L826-SFL1/L826-SFL1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L826-SFL1/L826-SFL1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L826-SFL1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L827-STP3/L827-STP3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L827-STP3/L827-STP3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L827-STP3.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L828-YRM1/L828-YRM1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L828-YRM1/L828-YRM1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L828-YRM1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L829-ISW2/L829-ISW2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L829-ISW2/L829-ISW2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L829-ISW2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L830-HTZ1/L830-HTZ1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L830-HTZ1/L830-HTZ1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L830-HTZ1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L831-PHD1/L831-PHD1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L831-PHD1/L831-PHD1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L831-PHD1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L832-SWI5/L832-SWI5.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L832-SWI5/L832-SWI5.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L832-SWI5/L832-SWI5.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L832-SWI5/L832-SWI5.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L832-SWI5.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L833-ACA1/L833-ACA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L833-ACA1/L833-ACA1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L833-ACA1/L833-ACA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L833-ACA1/L833-ACA1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L833-ACA1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L834-INO2/L834-INO2.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L834-INO2/L834-INO2.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L834-INO2/L834-INO2.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L834-INO2/L834-INO2.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L834-INO2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L835-PHO4/L835-PHO4.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L835-PHO4/L835-PHO4.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L835-PHO4/L835-PHO4.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L835-PHO4/L835-PHO4.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L835-PHO4.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L836-MGA1/L836-MGA1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L836-MGA1/L836-MGA1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L836-MGA1/L836-MGA1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L836-MGA1/L836-MGA1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L836-MGA1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L837-MIG1/L837-MIG1.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L837-MIG1/L837-MIG1.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L837-MIG1/L837-MIG1.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L837-MIG1/L837-MIG1.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L837-MIG1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L838-HAP3/L838-HAP3.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L838-HAP3/L838-HAP3.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L838-HAP3/L838-HAP3.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L838-HAP3/L838-HAP3.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L838-HAP3.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L839-YHR177W/L839-YHR177W.190731_NB551514_0236_AH7H75BGXC.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L839-YHR177W/L839-YHR177W.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L839-YHR177W/L839-YHR177W.190731_NB551514_0236_AH7H75BGXC.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L839-YHR177W/L839-YHR177W.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L839-YHR177W.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L847-GLN3/L847-GLN3.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L847-GLN3/L847-GLN3.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L847-GLN3.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L848-TOD6/L848-TOD6.190805_NB551514_0241_AHV7VLBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L848-TOD6/L848-TOD6.190805_NB551514_0241_AHV7VLBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L848-TOD6.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L925-MSN2-0min-rep1/L925-MSN2-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L925-MSN2-0min-rep1/L925-MSN2-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L925-MSN2-0min-rep1/L925-MSN2-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L925-MSN2-0min-rep1/L925-MSN2-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L925-MSN2-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L927-MSN1-0min-rep1/L927-MSN1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L927-MSN1-0min-rep1/L927-MSN1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L927-MSN1-0min-rep1/L927-MSN1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L927-MSN1-0min-rep1/L927-MSN1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L927-MSN1-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L928-HOG1-0min-rep1/L928-HOG1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L928-HOG1-0min-rep1/L928-HOG1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L928-HOG1-0min-rep1/L928-HOG1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L928-HOG1-0min-rep1/L928-HOG1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L928-HOG1-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L929-BDF1-0min-rep1/L929-BDF1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L929-BDF1-0min-rep1/L929-BDF1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L929-BDF1-0min-rep1/L929-BDF1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L929-BDF1-0min-rep1/L929-BDF1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L929-BDF1-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L930-YAP7-0min-rep1/L930-YAP7-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L930-YAP7-0min-rep1/L930-YAP7-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L930-YAP7-0min-rep1/L930-YAP7-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L930-YAP7-0min-rep1/L930-YAP7-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L930-YAP7-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L931-UME6-0min-rep1/L931-UME6-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L931-UME6-0min-rep1/L931-UME6-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L931-UME6-0min-rep1/L931-UME6-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L931-UME6-0min-rep1/L931-UME6-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L931-UME6-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L932-SMP1-0min-rep1/L932-SMP1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L932-SMP1-0min-rep1/L932-SMP1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L932-SMP1-0min-rep1/L932-SMP1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L932-SMP1-0min-rep1/L932-SMP1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L932-SMP1-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L933-YAP1-0min-rep1/L933-YAP1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L933-YAP1-0min-rep1/L933-YAP1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L933-YAP1-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L934-YAP3-0min-rep1/L934-YAP3-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L934-YAP3-0min-rep1/L934-YAP3-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L934-YAP3-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L935-ARR1-0min-rep1/L935-ARR1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L935-ARR1-0min-rep1/L935-ARR1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L935-ARR1-0min-rep1/L935-ARR1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L935-ARR1-0min-rep1/L935-ARR1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L935-ARR1-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L936-PHO4-0min-rep1/L936-PHO4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L936-PHO4-0min-rep1/L936-PHO4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L936-PHO4-0min-rep1/L936-PHO4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L936-PHO4-0min-rep1/L936-PHO4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L936-PHO4-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L937-YAP6-0min-rep1/L937-YAP6-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L937-YAP6-0min-rep1/L937-YAP6-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L937-YAP6-0min-rep1/L937-YAP6-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L937-YAP6-0min-rep1/L937-YAP6-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L937-YAP6-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L938-PDR3-0min-rep1/L938-PDR3-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L938-PDR3-0min-rep1/L938-PDR3-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L938-PDR3-0min-rep1/L938-PDR3-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L938-PDR3-0min-rep1/L938-PDR3-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L938-PDR3-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L939-GAT1-0min-rep1/L939-GAT1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L939-GAT1-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L940-SKO1-0min-rep1/L940-SKO1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L940-SKO1-0min-rep1/L940-SKO1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L940-SKO1-0min-rep1/L940-SKO1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L940-SKO1-0min-rep1/L940-SKO1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L940-SKO1-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L941-CHA4-0min-rep1/L941-CHA4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L941-CHA4-0min-rep1/L941-CHA4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L941-CHA4-0min-rep1/L941-CHA4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L941-CHA4-0min-rep1/L941-CHA4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L941-CHA4-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L942-PHO2-0min-rep1/L942-PHO2-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L942-PHO2-0min-rep1/L942-PHO2-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L942-PHO2-0min-rep1/L942-PHO2-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L942-PHO2-0min-rep1/L942-PHO2-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L942-PHO2-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L943-ROX1-0min-rep1/L943-ROX1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L943-ROX1-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L944-HOT1-0min-rep1/L944-HOT1-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L944-HOT1-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L945-YAP5-0min-rep1/L945-YAP5-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L945-YAP5-0min-rep1/L945-YAP5-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L945-YAP5-0min-rep1/L945-YAP5-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L945-YAP5-0min-rep1/L945-YAP5-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L945-YAP5-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L946-GAT4-0min-rep1/L946-GAT4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L946-GAT4-0min-rep1/L946-GAT4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L946-GAT4-0min-rep1/L946-GAT4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L946-GAT4-0min-rep1/L946-GAT4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L946-GAT4-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L947-SKN7-0min-rep1/L947-SKN7-0min-rep1.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L947-SKN7-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L948-MSN4-0min-rep1/L948-MSN4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L948-MSN4-0min-rep1/L948-MSN4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L948-MSN4-0min-rep1/L948-MSN4-0min-rep1.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L948-MSN4-0min-rep1/L948-MSN4-0min-rep1.190912_NB551514_0273_AHTWVGBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L948-MSN4-0min-rep1.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L973-HOT1-0min-rep2/L973-HOT1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L973-HOT1-0min-rep2/L973-HOT1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L973-HOT1-0min-rep2/L973-HOT1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L973-HOT1-0min-rep2/L973-HOT1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L973-HOT1-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L974-ROX1-0min-rep2/L974-ROX1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L974-ROX1-0min-rep2/L974-ROX1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L974-ROX1-0min-rep2/L974-ROX1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L974-ROX1-0min-rep2/L974-ROX1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L974-ROX1-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L975-PHO2-0min-rep2/L975-PHO2-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L975-PHO2-0min-rep2/L975-PHO2-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L975-PHO2-0min-rep2/L975-PHO2-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L975-PHO2-0min-rep2/L975-PHO2-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L975-PHO2-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L976-CHA4-0min-rep2/L976-CHA4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L976-CHA4-0min-rep2/L976-CHA4-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L976-CHA4-0min-rep2/L976-CHA4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L976-CHA4-0min-rep2/L976-CHA4-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L976-CHA4-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L977-GAT4-0min-rep2/L977-GAT4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L977-GAT4-0min-rep2/L977-GAT4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L977-GAT4-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L978-YAP5-0min-rep2/L978-YAP5-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L978-YAP5-0min-rep2/L978-YAP5-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L978-YAP5-0min-rep2/L978-YAP5-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L978-YAP5-0min-rep2/L978-YAP5-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L978-YAP5-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L979-MSN2-0min-rep2/L979-MSN2-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L979-MSN2-0min-rep2/L979-MSN2-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L979-MSN2-0min-rep2/L979-MSN2-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L979-MSN2-0min-rep2/L979-MSN2-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L979-MSN2-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L980-BDF1-0min-rep2/L980-BDF1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L980-BDF1-0min-rep2/L980-BDF1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L980-BDF1-0min-rep2/L980-BDF1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L980-BDF1-0min-rep2/L980-BDF1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L980-BDF1-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L981-SFP1-0min-rep2/L981-SFP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L981-SFP1-0min-rep2/L981-SFP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L981-SFP1-0min-rep2/L981-SFP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L981-SFP1-0min-rep2/L981-SFP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L981-SFP1-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L982-SKN7-0min-rep2/L982-SKN7-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L982-SKN7-0min-rep2/L982-SKN7-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L982-SKN7-0min-rep2/L982-SKN7-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L982-SKN7-0min-rep2/L982-SKN7-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L982-SKN7-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L983-PDR3-0min-rep2/L983-PDR3-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L983-PDR3-0min-rep2/L983-PDR3-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L983-PDR3-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L984-HOG1-0min-rep2/L984-HOG1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L984-HOG1-0min-rep2/L984-HOG1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L984-HOG1-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L985-YAP3-0min-rep2/L985-YAP3-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L985-YAP3-0min-rep2/L985-YAP3-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L985-YAP3-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L986-MSN1-0min-rep2/L986-MSN1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L986-MSN1-0min-rep2/L986-MSN1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L986-MSN1-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L987-MSN4-0min-rep2/L987-MSN4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L987-MSN4-0min-rep2/L987-MSN4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L987-MSN4-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L988-YAP6-0min-rep2/L988-YAP6-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L988-YAP6-0min-rep2/L988-YAP6-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L988-YAP6-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L989-YAP1-0min-rep2/L989-YAP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L989-YAP1-0min-rep2/L989-YAP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L989-YAP1-0min-rep2/L989-YAP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L989-YAP1-0min-rep2/L989-YAP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L989-YAP1-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L990-SMP1-0min-rep2/L990-SMP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L990-SMP1-0min-rep2/L990-SMP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L990-SMP1-0min-rep2/L990-SMP1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L990-SMP1-0min-rep2/L990-SMP1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L990-SMP1-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L991-ARR1-0min-rep2/L991-ARR1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L991-ARR1-0min-rep2/L991-ARR1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L991-ARR1-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L992-UME6-0min-rep2/L992-UME6-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L992-UME6-0min-rep2/L992-UME6-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L992-UME6-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L993-PHO4-0min-rep2/L993-PHO4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L993-PHO4-0min-rep2/L993-PHO4-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L993-PHO4-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L994-SKO1-0min-rep2/L994-SKO1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L994-SKO1-0min-rep2/L994-SKO1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L994-SKO1-0min-rep2/L994-SKO1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L994-SKO1-0min-rep2/L994-SKO1-0min-rep2.190914_NB551514_0275_AHV3KWBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L994-SKO1-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L995-YAP7-0min-rep2/L995-YAP7-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L995-YAP7-0min-rep2/L995-YAP7-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L995-YAP7-0min-rep2.2x10mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L996-GAT1-0min-rep2/L996-GAT1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L996-GAT1-0min-rep2/L996-GAT1-0min-rep2.190910_NB551514_0271_AHMLWFBGXB.end2.fastq.gz -trim 10 10 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L996-GAT1-0min-rep2.2x10mers.unique