zcat /scratch/PI/wjg/alex/neuron/chip/chang/JA26-1417-Foxg1-ChIP_S1_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/greenleaf/JA26-1417-Foxg1-ChIP_S1_L001_R1_001.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA26-1417-Foxg1-ChIP.36mers.hg19-male.unique
zcat /scratch/PI/wjg/alex/neuron/chip/chang/JA26-1417-Foxg1-Input_S5_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/greenleaf/JA26-1417-Foxg1-Input_S5_L001_R1_001.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA26-1417-Foxg1-Input.36mers.hg19-male.unique
zcat /scratch/PI/wjg/alex/neuron/chip/chang/JA26-8738-Foxg1-ChIP_S2_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/greenleaf/JA26-8738-Foxg1-ChIP_S2_L001_R1_001.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA26-8738-Foxg1-ChIP.36mers.hg19-male.unique
zcat /scratch/PI/wjg/alex/neuron/chip/chang/JA26-8738-Foxg1-Input_S6_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/greenleaf/JA26-8738-Foxg1-Input_S6_L001_R1_001.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA26-8738-Foxg1-Input.36mers.hg19-male.unique
zcat /scratch/PI/wjg/alex/neuron/chip/chang/JA27-1417-Foxg1-ChIP_S3_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/greenleaf/JA27-1417-Foxg1-ChIP_S3_L001_R1_001.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA27-1417-Foxg1-ChIP.36mers.hg19-male.unique
zcat /scratch/PI/wjg/alex/neuron/chip/chang/JA27-1417-Foxg1-Input_S7_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/greenleaf/JA27-1417-Foxg1-Input_S7_L001_R1_001.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA27-1417-Foxg1-Input.36mers.hg19-male.unique
zcat /scratch/PI/wjg/alex/neuron/chip/chang/JA27-8738-Foxg1-ChIP_S4_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/greenleaf/JA27-8738-Foxg1-ChIP_S4_L001_R1_001.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA27-8738-Foxg1-ChIP.36mers.hg19-male.unique
zcat /scratch/PI/wjg/alex/neuron/chip/chang/JA27-8738-Foxg1-Input_S8_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/greenleaf/JA27-8738-Foxg1-Input_S8_L001_R1_001.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA27-8738-Foxg1-Input.36mers.hg19-male.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /scratch/PI/wjg/alex/neuron/chip/chang/JA26-1417-Foxg1-ChIP_S1_L001_R1_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA26-1417-Foxg1-ChIP_S1_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/chang/JA26-1417-Foxg1-ChIP_S1_L001_R2_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA26-1417-Foxg1-ChIP_S1_L001_R2_001.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/hg19/bowtie-indexes/hg19-female -p 8 -v 3 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA26-1417-Foxg1-ChIP.2x36mers.hg19-male.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /scratch/PI/wjg/alex/neuron/chip/chang/JA26-1417-Foxg1-Input_S5_L001_R1_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA26-1417-Foxg1-Input_S5_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/chang/JA26-1417-Foxg1-Input_S5_L001_R2_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA26-1417-Foxg1-Input_S5_L001_R2_001.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/hg19/bowtie-indexes/hg19-female -p 8 -v 3 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA26-1417-Foxg1-Input.2x36mers.hg19-male.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /scratch/PI/wjg/alex/neuron/chip/chang/JA26-8738-Foxg1-ChIP_S2_L001_R1_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA26-8738-Foxg1-ChIP_S2_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/chang/JA26-8738-Foxg1-ChIP_S2_L001_R2_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA26-8738-Foxg1-ChIP_S2_L001_R2_001.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/hg19/bowtie-indexes/hg19-female -p 8 -v 3 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA26-8738-Foxg1-ChIP.2x36mers.hg19-male.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /scratch/PI/wjg/alex/neuron/chip/chang/JA26-8738-Foxg1-Input_S6_L001_R1_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA26-8738-Foxg1-Input_S6_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/chang/JA26-8738-Foxg1-Input_S6_L001_R2_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA26-8738-Foxg1-Input_S6_L001_R2_001.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/hg19/bowtie-indexes/hg19-female -p 8 -v 3 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA26-8738-Foxg1-Input.2x36mers.hg19-male.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /scratch/PI/wjg/alex/neuron/chip/chang/JA27-1417-Foxg1-ChIP_S3_L001_R1_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA27-1417-Foxg1-ChIP_S3_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/chang/JA27-1417-Foxg1-ChIP_S3_L001_R2_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA27-1417-Foxg1-ChIP_S3_L001_R2_001.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/hg19/bowtie-indexes/hg19-female -p 8 -v 3 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA27-1417-Foxg1-ChIP.2x36mers.hg19-male.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /scratch/PI/wjg/alex/neuron/chip/chang/JA27-1417-Foxg1-Input_S7_L001_R1_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA27-1417-Foxg1-Input_S7_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/chang/JA27-1417-Foxg1-Input_S7_L001_R2_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA27-1417-Foxg1-Input_S7_L001_R2_001.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/hg19/bowtie-indexes/hg19-female -p 8 -v 3 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA27-1417-Foxg1-Input.2x36mers.hg19-male.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /scratch/PI/wjg/alex/neuron/chip/chang/JA27-8738-Foxg1-ChIP_S4_L001_R1_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA27-8738-Foxg1-ChIP_S4_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/chang/JA27-8738-Foxg1-ChIP_S4_L001_R2_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA27-8738-Foxg1-ChIP_S4_L001_R2_001.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/hg19/bowtie-indexes/hg19-female -p 8 -v 3 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA27-8738-Foxg1-ChIP.2x36mers.hg19-male.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /scratch/PI/wjg/alex/neuron/chip/chang/JA27-8738-Foxg1-Input_S8_L001_R1_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA27-8738-Foxg1-Input_S8_L001_R1_001.fastq.gz /scratch/PI/wjg/alex/neuron/chip/chang/JA27-8738-Foxg1-Input_S8_L001_R2_001.fastq.gz,/scratch/PI/wjg/alex/neuron/chip/greenleaf/JA27-8738-Foxg1-Input_S8_L001_R2_001.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/hg19/bowtie-indexes/hg19-female -p 8 -v 3 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - JA27-8738-Foxg1-Input.2x36mers.hg19-male.unique