python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C1_gDNA_rep1-GSM2434317/SRR5123141_1.fastq.gz C1_gDNA_rep1-GSM2434317/SRR5123141_2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C1_gDNA_rep1-GSM2434317/all.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C1_gDNA_rep2-GSM2434318/SRR5123142_1.fastq.gz C1_gDNA_rep2-GSM2434318/SRR5123142_2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -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 ~/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C1_gDNA_rep2-GSM2434318/all.2x36mers.hg19.unique