python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MNase-GAF-RNAi-Rep1-GSM1423060/SRR1503611_1.fastq.gz MNase-GAF-RNAi-Rep1-GSM1423060/SRR1503611_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/dm3/bowtie-indexes/dm3 -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/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MNase-GAF-RNAi-Rep1-GSM1423060.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MNase-GAF-RNAi-Rep2-GSM1423061/SRR1503612_1.fastq.gz MNase-GAF-RNAi-Rep2-GSM1423061/SRR1503612_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/dm3/bowtie-indexes/dm3 -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/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MNase-GAF-RNAi-Rep2-GSM1423061.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MNase-GAF-RNAi-Rep3-GSM1423062/SRR1503613_1.fastq.gz MNase-GAF-RNAi-Rep3-GSM1423062/SRR1503613_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/dm3/bowtie-indexes/dm3 -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/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MNase-GAF-RNAi-Rep3-GSM1423062.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MNase-LacZ-RNAi-Rep1-GSM1423057/SRR1503608_1.fastq.gz MNase-LacZ-RNAi-Rep1-GSM1423057/SRR1503608_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/dm3/bowtie-indexes/dm3 -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/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MNase-LacZ-RNAi-Rep1-GSM1423057.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MNase-LacZ-RNAi-Rep2-GSM1423058/SRR1503609_1.fastq.gz MNase-LacZ-RNAi-Rep2-GSM1423058/SRR1503609_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/dm3/bowtie-indexes/dm3 -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/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MNase-LacZ-RNAi-Rep2-GSM1423058.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MNase-LacZ-RNAi-Rep3-GSM1423059/SRR1503610_1.fastq.gz MNase-LacZ-RNAi-Rep3-GSM1423059/SRR1503610_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/dm3/bowtie-indexes/dm3 -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/dm3/bowtie-indexes/dm3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MNase-LacZ-RNAi-Rep3-GSM1423059.2x36mers.unique