python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3844-K562_Input.250612_NB551514_0305_AH3YCCBGYX.end1.fastq.gz L3844-K562_Input.250612_NB551514_0305_AH3YCCBGYX.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 - L3844-K562_Input.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3845-Julia1_Input.250612_NB551514_0305_AH3YCCBGYX.end1.fastq.gz L3845-Julia1_Input.250612_NB551514_0305_AH3YCCBGYX.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 - L3845-Julia1_Input.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3846-Julia2_Input.250612_NB551514_0305_AH3YCCBGYX.end1.fastq.gz L3846-Julia2_Input.250612_NB551514_0305_AH3YCCBGYX.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 - L3846-Julia2_Input.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3847-K562_KLF1-PA5-86441.250612_NB551514_0305_AH3YCCBGYX.end1.fastq.gz L3847-K562_KLF1-PA5-86441.250612_NB551514_0305_AH3YCCBGYX.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 - L3847-K562_KLF1-PA5-86441.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3848-Julia1_KLF1-PA5-86441.250612_NB551514_0305_AH3YCCBGYX.end1.fastq.gz L3848-Julia1_KLF1-PA5-86441.250612_NB551514_0305_AH3YCCBGYX.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 - L3848-Julia1_KLF1-PA5-86441.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3849-K562_KLF1-NB100-1019.250612_NB551514_0305_AH3YCCBGYX.end1.fastq.gz L3849-K562_KLF1-NB100-1019.250612_NB551514_0305_AH3YCCBGYX.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 - L3849-K562_KLF1-NB100-1019.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3850-Julia2_KLF1-NB100-1019.250612_NB551514_0305_AH3YCCBGYX.end1.fastq.gz L3850-Julia2_KLF1-NB100-1019.250612_NB551514_0305_AH3YCCBGYX.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 - L3850-Julia2_KLF1-NB100-1019.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3851-Julia1_KLF1-H00010661.250612_NB551514_0305_AH3YCCBGYX.end1.fastq.gz L3851-Julia1_KLF1-H00010661.250612_NB551514_0305_AH3YCCBGYX.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 - L3851-Julia1_KLF1-H00010661.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L3852-Julia2_KLF1-H00010661.250612_NB551514_0305_AH3YCCBGYX.end1.fastq.gz L3852-Julia2_KLF1-H00010661.250612_NB551514_0305_AH3YCCBGYX.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 - L3852-Julia2_KLF1-H00010661.2x36mers.unique