python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Input_rep1-GSM2787575-1_1.fastq.gz,Input_rep1-GSM2787575-2_1.fastq.gz,Input_rep1-GSM2787575-3_1.fastq.gz,Input_rep1-GSM2787575-4_1.fastq.gz Input_rep1-GSM2787575-1_2.fastq.gz,Input_rep1-GSM2787575-2_2.fastq.gz,Input_rep1-GSM2787575-3_2.fastq.gz,Input_rep1-GSM2787575-4_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 - Input_rep1-GSM2787575.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Input_rep2-GSM2787576-1_1.fastq.gz,Input_rep2-GSM2787576-2_1.fastq.gz,Input_rep2-GSM2787576-3_1.fastq.gz,Input_rep2-GSM2787576-4_1.fastq.gz Input_rep2-GSM2787576-1_2.fastq.gz,Input_rep2-GSM2787576-2_2.fastq.gz,Input_rep2-GSM2787576-3_2.fastq.gz,Input_rep2-GSM2787576-4_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 - Input_rep2-GSM2787576.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Input_rep3-GSM2787577-1_1.fastq.gz,Input_rep3-GSM2787577-2_1.fastq.gz,Input_rep3-GSM2787577-3_1.fastq.gz,Input_rep3-GSM2787577-4_1.fastq.gz Input_rep3-GSM2787577-1_2.fastq.gz,Input_rep3-GSM2787577-2_2.fastq.gz,Input_rep3-GSM2787577-3_2.fastq.gz,Input_rep3-GSM2787577-4_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 - Input_rep3-GSM2787577.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Input_rep4-GSM2787578-1_1.fastq.gz,Input_rep4-GSM2787578-2_1.fastq.gz,Input_rep4-GSM2787578-3_1.fastq.gz,Input_rep4-GSM2787578-4_1.fastq.gz Input_rep4-GSM2787578-1_2.fastq.gz,Input_rep4-GSM2787578-2_2.fastq.gz,Input_rep4-GSM2787578-3_2.fastq.gz,Input_rep4-GSM2787578-4_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 - Input_rep4-GSM2787578.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Input_rep5-GSM2787579-1_1.fastq.gz,Input_rep5-GSM2787579-2_1.fastq.gz,Input_rep5-GSM2787579-3_1.fastq.gz,Input_rep5-GSM2787579-4_1.fastq.gz Input_rep5-GSM2787579-1_2.fastq.gz,Input_rep5-GSM2787579-2_2.fastq.gz,Input_rep5-GSM2787579-3_2.fastq.gz,Input_rep5-GSM2787579-4_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 - Input_rep5-GSM2787579.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py STARR_rep1-GSM2787580-1_1.fastq.gz,STARR_rep1-GSM2787580-2_1.fastq.gz,STARR_rep1-GSM2787580-3_1.fastq.gz,STARR_rep1-GSM2787580-4_1.fastq.gz STARR_rep1-GSM2787580-1_2.fastq.gz,STARR_rep1-GSM2787580-2_2.fastq.gz,STARR_rep1-GSM2787580-3_2.fastq.gz,STARR_rep1-GSM2787580-4_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 - STARR_rep1-GSM2787580.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py STARR_rep2-GSM2787581-1_1.fastq.gz,STARR_rep2-GSM2787581-2_1.fastq.gz,STARR_rep2-GSM2787581-3_1.fastq.gz,STARR_rep2-GSM2787581-4_1.fastq.gz STARR_rep2-GSM2787581-1_2.fastq.gz,STARR_rep2-GSM2787581-2_2.fastq.gz,STARR_rep2-GSM2787581-3_2.fastq.gz,STARR_rep2-GSM2787581-4_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 - STARR_rep2-GSM2787581.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py STARR_rep3-GSM2787582-1_1.fastq.gz,STARR_rep3-GSM2787582-2_1.fastq.gz,STARR_rep3-GSM2787582-3_1.fastq.gz,STARR_rep3-GSM2787582-4_1.fastq.gz STARR_rep3-GSM2787582-1_2.fastq.gz,STARR_rep3-GSM2787582-2_2.fastq.gz,STARR_rep3-GSM2787582-3_2.fastq.gz,STARR_rep3-GSM2787582-4_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 - STARR_rep3-GSM2787582.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py STARR_rep4-GSM2787583-1_1.fastq.gz,STARR_rep4-GSM2787583-2_1.fastq.gz,STARR_rep4-GSM2787583-3_1.fastq.gz,STARR_rep4-GSM2787583-4_1.fastq.gz STARR_rep4-GSM2787583-1_2.fastq.gz,STARR_rep4-GSM2787583-2_2.fastq.gz,STARR_rep4-GSM2787583-3_2.fastq.gz,STARR_rep4-GSM2787583-4_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 - STARR_rep4-GSM2787583.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py STARR_rep5-GSM2787584-1_1.fastq.gz,STARR_rep5-GSM2787584-2_1.fastq.gz,STARR_rep5-GSM2787584-3_1.fastq.gz,STARR_rep5-GSM2787584-4_1.fastq.gz STARR_rep5-GSM2787584-1_2.fastq.gz,STARR_rep5-GSM2787584-2_2.fastq.gz,STARR_rep5-GSM2787584-3_2.fastq.gz,STARR_rep5-GSM2787584-4_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 - STARR_rep5-GSM2787584.2x36mers.unique