python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L5486-AS_NRSF.260221_NB551514_0408_AHCJ27BGY2.end1.fastq.gz L5486-AS_NRSF.260221_NB551514_0408_AHCJ27BGY2.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 - L5486-AS_NRSF.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L5487-HS_NRSF.260221_NB551514_0408_AHCJ27BGY2.end1.fastq.gz L5487-HS_NRSF.260221_NB551514_0408_AHCJ27BGY2.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 - L5487-HS_NRSF.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L5488-UT_NRSF.260221_NB551514_0408_AHCJ27BGY2.end1.fastq.gz L5488-UT_NRSF.260221_NB551514_0408_AHCJ27BGY2.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 - L5488-UT_NRSF.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L5489-HEK_SPI1_0.75_SPI_ChIP.260221_NB551514_0408_AHCJ27BGY2.end1.fastq.gz L5489-HEK_SPI1_0.75_SPI_ChIP.260221_NB551514_0408_AHCJ27BGY2.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 - L5489-HEK_SPI1_0.75_SPI_ChIP.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L5490-HEK_SOX2_0.75_SOX_ChIP.260221_NB551514_0408_AHCJ27BGY2.end1.fastq.gz L5490-HEK_SOX2_0.75_SOX_ChIP.260221_NB551514_0408_AHCJ27BGY2.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 - L5490-HEK_SOX2_0.75_SOX_ChIP.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L5491-HEK_IRF4_0.75_IRF4_ChIP.260221_NB551514_0408_AHCJ27BGY2.end1.fastq.gz L5491-HEK_IRF4_0.75_IRF4_ChIP.260221_NB551514_0408_AHCJ27BGY2.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 - L5491-HEK_IRF4_0.75_IRF4_ChIP.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L5492-HEK_LEF1_0.75_LEF1_ChIP.260221_NB551514_0408_AHCJ27BGY2.end1.fastq.gz L5492-HEK_LEF1_0.75_LEF1_ChIP.260221_NB551514_0408_AHCJ27BGY2.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 - L5492-HEK_LEF1_0.75_LEF1_ChIP.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L5493-HEK_ALX4_0.75_ALX4-FLAG_ChIP.260221_NB551514_0408_AHCJ27BGY2.end1.fastq.gz L5493-HEK_ALX4_0.75_ALX4-FLAG_ChIP.260221_NB551514_0408_AHCJ27BGY2.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 - L5493-HEK_ALX4_0.75_ALX4-FLAG_ChIP.2x36mers.unique