python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3818-B-HP_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end1.fastq.gz,L3818-B-HP_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3818-B-HP_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end2.fastq.gz,L3818-B-HP_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3818-B-HP_NRSF1.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3819-B-HP_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end1.fastq.gz,L3819-B-HP_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3819-B-HP_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end2.fastq.gz,L3819-B-HP_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3819-B-HP_NRSF1.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3820-B-O_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end1.fastq.gz,L3820-B-O_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3820-B-O_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end2.fastq.gz,L3820-B-O_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3820-B-O_NRSF1.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3821-B-O_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end1.fastq.gz,L3821-B-O_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3821-B-O_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end2.fastq.gz,L3821-B-O_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3821-B-O_NRSF1.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3822-U-HP_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end1.fastq.gz,L3822-U-HP_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3822-U-HP_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end2.fastq.gz,L3822-U-HP_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3822-U-HP_NRSF1.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3823-U-HP_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end1.fastq.gz,L3823-U-HP_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3823-U-HP_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end2.fastq.gz,L3823-U-HP_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3823-U-HP_NRSF1.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3824-U-O_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end1.fastq.gz,L3824-U-O_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3824-U-O_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end2.fastq.gz,L3824-U-O_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3824-U-O_NRSF1.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3825-U-O_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end1.fastq.gz,L3825-U-O_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3825-U-O_NRSF1.250427_NB551514_0288_AHWFCJBGYW.end2.fastq.gz,L3825-U-O_NRSF1.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3825-U-O_NRSF1.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3969-K562_KLF1-PA5-86441.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3969-K562_KLF1-PA5-86441.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3969-K562_KLF1-PA5-86441.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3970-K562_KLF1-PA5-86441.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3970-K562_KLF1-PA5-86441.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3970-K562_KLF1-PA5-86441.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3971-K562_KLF1-NB100-1019.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3971-K562_KLF1-NB100-1019.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3971-K562_KLF1-NB100-1019.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3972-K562_KLF1-NB100-1019_H00010661.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3972-K562_KLF1-NB100-1019_H00010661.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3972-K562_KLF1-NB100-1019_H00010661.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3973-K562_KLF1-H00010661.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3973-K562_KLF1-H00010661.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3973-K562_KLF1-H00010661.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3974-K562-Pol2-4H8.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3974-K562-Pol2-4H8.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3974-K562-Pol2-4H8.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3975-K562-H3K27ac.250623_NB551514_0310_AHHLN2BGXW.end1.fastq.gz L3975-K562-H3K27ac.250623_NB551514_0310_AHHLN2BGXW.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3975-K562-H3K27ac.2x36mers.unique