python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py A549-eGFP-FOSL2-ChIP-SCGPM_SReq-1140_HK23F_L8-ATCACG_R1.fastq.gz A549-eGFP-FOSL2-ChIP-SCGPM_SReq-1140_HK23F_L8-ATCACG_R2.fastq.gz -trim 25 25 | /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 -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 - A549-eGFP-FOSL2-ChIP-SCGPM_SReq-1140_HK23F_L8-ATCACG.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py A549-eGFP-FOSL2-ChIP-SCGPM_SReq-1140_HK23F_L8_CGATGT_R1.fastq.gz A549-eGFP-FOSL2-ChIP-SCGPM_SReq-1140_HK23F_L8_CGATGT_R2.fastq.gz -trim 25 25 | /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 -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 - A549-eGFP-FOSL2-ChIP-SCGPM_SReq-1140_HK23F_L8_CGATGT.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py A549-eGFP-FOSL2-Input-SCGPM_SReq-1140_HK23F_L8_CAGATC_R1.fastq.gz A549-eGFP-FOSL2-Input-SCGPM_SReq-1140_HK23F_L8_CGATGT_R2.fastq.gz -trim 25 25 | /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 -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 - A549-eGFP-FOSL2-Input-SCGPM_SReq-1140_HK23F_L8_CAGATC.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py A549-eGFP-FOSL2-ChIP-SCGPM_SReq-1140_HK23F_L8-ATCACG_R1.fastq.gz 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-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-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - A549-eGFP-FOSL2-ChIP-SCGPM_SReq-1140_HK23F_L8-ATCACG.1x36mers.hg19.unique 
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py A549-eGFP-FOSL2-ChIP-SCGPM_SReq-1140_HK23F_L8_CGATGT_R1.fastq.gz 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-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-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - A549-eGFP-FOSL2-ChIP-SCGPM_SReq-1140_HK23F_L8_CGATGT.1x36mers.hg19.unique 
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py A549-eGFP-FOSL2-Input-SCGPM_SReq-1140_HK23F_L8_CAGATC_R1.fastq.gz 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-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-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - A549-eGFP-FOSL2-Input-SCGPM_SReq-1140_HK23F_L8_CAGATC.1x36mers.hg19.unique