python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Population_STARR-seq_Input_Plasmid_Library-GSM2058394/SRR3157992_1.fastq.gz Population_STARR-seq_Input_Plasmid_Library-GSM2058394/SRR3157992_2.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 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Population_STARR-seq_Input_Plasmid_Library-GSM2058394/alignments.2x36mers.unique.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Population_STARR-seq_Rep1-GSM2058391/SRR3157989_1.fastq.gz Population_STARR-seq_Rep1-GSM2058391/SRR3157989_2.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 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Population_STARR-seq_Rep1-GSM2058391/alignments.2x36mers.unique.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Population_STARR-seq_Rep2-GSM2058392/SRR3157990_1.fastq.gz Population_STARR-seq_Rep2-GSM2058392/SRR3157990_2.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 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Population_STARR-seq_Rep2-GSM2058392/alignments.2x36mers.unique.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Population_STARR-seq_Rep3-GSM2058393/SRR3157991_1.fastq.gz Population_STARR-seq_Rep3-GSM2058393/SRR3157991_2.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 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Population_STARR-seq_Rep3-GSM2058393/alignments.2x36mers.unique.bam