python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq0.gz Chemical-GSM2183909.end2.fastq0.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.0
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq100.gz Chemical-GSM2183909.end2.fastq100.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.100
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq101.gz Chemical-GSM2183909.end2.fastq101.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.101
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq102.gz Chemical-GSM2183909.end2.fastq102.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.102
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq103.gz Chemical-GSM2183909.end2.fastq103.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.103
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq104.gz Chemical-GSM2183909.end2.fastq104.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.104
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq105.gz Chemical-GSM2183909.end2.fastq105.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.105
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq106.gz Chemical-GSM2183909.end2.fastq106.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.106
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq107.gz Chemical-GSM2183909.end2.fastq107.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.107
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq108.gz Chemical-GSM2183909.end2.fastq108.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.108
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq109.gz Chemical-GSM2183909.end2.fastq109.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.109
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq10.gz Chemical-GSM2183909.end2.fastq10.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.10
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq110.gz Chemical-GSM2183909.end2.fastq110.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.110
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq111.gz Chemical-GSM2183909.end2.fastq111.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.111
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq112.gz Chemical-GSM2183909.end2.fastq112.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.112
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq113.gz Chemical-GSM2183909.end2.fastq113.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.113
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq114.gz Chemical-GSM2183909.end2.fastq114.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.114
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq115.gz Chemical-GSM2183909.end2.fastq115.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.115
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq116.gz Chemical-GSM2183909.end2.fastq116.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.116
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq117.gz Chemical-GSM2183909.end2.fastq117.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.117
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq118.gz Chemical-GSM2183909.end2.fastq118.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.118
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq119.gz Chemical-GSM2183909.end2.fastq119.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.119
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq11.gz Chemical-GSM2183909.end2.fastq11.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.11
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq120.gz Chemical-GSM2183909.end2.fastq120.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.120
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq121.gz Chemical-GSM2183909.end2.fastq121.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.121
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq122.gz Chemical-GSM2183909.end2.fastq122.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.122
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq123.gz Chemical-GSM2183909.end2.fastq123.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.123
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq124.gz Chemical-GSM2183909.end2.fastq124.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.124
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq125.gz Chemical-GSM2183909.end2.fastq125.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.125
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq126.gz Chemical-GSM2183909.end2.fastq126.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.126
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq127.gz Chemical-GSM2183909.end2.fastq127.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.127
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq128.gz Chemical-GSM2183909.end2.fastq128.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.128
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq129.gz Chemical-GSM2183909.end2.fastq129.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.129
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq12.gz Chemical-GSM2183909.end2.fastq12.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.12
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq130.gz Chemical-GSM2183909.end2.fastq130.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.130
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq131.gz Chemical-GSM2183909.end2.fastq131.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.131
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq132.gz Chemical-GSM2183909.end2.fastq132.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.132
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq133.gz Chemical-GSM2183909.end2.fastq133.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.133
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq134.gz Chemical-GSM2183909.end2.fastq134.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.134
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq135.gz Chemical-GSM2183909.end2.fastq135.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.135
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq136.gz Chemical-GSM2183909.end2.fastq136.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.136
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq137.gz Chemical-GSM2183909.end2.fastq137.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.137
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq138.gz Chemical-GSM2183909.end2.fastq138.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.138
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq139.gz Chemical-GSM2183909.end2.fastq139.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.139
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq13.gz Chemical-GSM2183909.end2.fastq13.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.13
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq140.gz Chemical-GSM2183909.end2.fastq140.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.140
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq141.gz Chemical-GSM2183909.end2.fastq141.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.141
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq142.gz Chemical-GSM2183909.end2.fastq142.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.142
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq143.gz Chemical-GSM2183909.end2.fastq143.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.143
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq144.gz Chemical-GSM2183909.end2.fastq144.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.144
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq145.gz Chemical-GSM2183909.end2.fastq145.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.145
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq146.gz Chemical-GSM2183909.end2.fastq146.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.146
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq147.gz Chemical-GSM2183909.end2.fastq147.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.147
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq148.gz Chemical-GSM2183909.end2.fastq148.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.148
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq149.gz Chemical-GSM2183909.end2.fastq149.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.149
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq14.gz Chemical-GSM2183909.end2.fastq14.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.14
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq150.gz Chemical-GSM2183909.end2.fastq150.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.150
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq151.gz Chemical-GSM2183909.end2.fastq151.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.151
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq152.gz Chemical-GSM2183909.end2.fastq152.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.152
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq153.gz Chemical-GSM2183909.end2.fastq153.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.153
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq154.gz Chemical-GSM2183909.end2.fastq154.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.154
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq155.gz Chemical-GSM2183909.end2.fastq155.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.155
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq156.gz Chemical-GSM2183909.end2.fastq156.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.156
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq157.gz Chemical-GSM2183909.end2.fastq157.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.157
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq158.gz Chemical-GSM2183909.end2.fastq158.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.158
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq159.gz Chemical-GSM2183909.end2.fastq159.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.159
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq15.gz Chemical-GSM2183909.end2.fastq15.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.15
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq160.gz Chemical-GSM2183909.end2.fastq160.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.160
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq161.gz Chemical-GSM2183909.end2.fastq161.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.161
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq162.gz Chemical-GSM2183909.end2.fastq162.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.162
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq163.gz Chemical-GSM2183909.end2.fastq163.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.163
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq164.gz Chemical-GSM2183909.end2.fastq164.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.164
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq165.gz Chemical-GSM2183909.end2.fastq165.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.165
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq166.gz Chemical-GSM2183909.end2.fastq166.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.166
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq167.gz Chemical-GSM2183909.end2.fastq167.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.167
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq168.gz Chemical-GSM2183909.end2.fastq168.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.168
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq169.gz Chemical-GSM2183909.end2.fastq169.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.169
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq16.gz Chemical-GSM2183909.end2.fastq16.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.16
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq170.gz Chemical-GSM2183909.end2.fastq170.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.170
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq171.gz Chemical-GSM2183909.end2.fastq171.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.171
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq172.gz Chemical-GSM2183909.end2.fastq172.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.172
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq173.gz Chemical-GSM2183909.end2.fastq173.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.173
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq174.gz Chemical-GSM2183909.end2.fastq174.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.174
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq175.gz Chemical-GSM2183909.end2.fastq175.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.175
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq176.gz Chemical-GSM2183909.end2.fastq176.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.176
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq177.gz Chemical-GSM2183909.end2.fastq177.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.177
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq178.gz Chemical-GSM2183909.end2.fastq178.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.178
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq179.gz Chemical-GSM2183909.end2.fastq179.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.179
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq17.gz Chemical-GSM2183909.end2.fastq17.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.17
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq180.gz Chemical-GSM2183909.end2.fastq180.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.180
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq181.gz Chemical-GSM2183909.end2.fastq181.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.181
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq182.gz Chemical-GSM2183909.end2.fastq182.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.182
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq183.gz Chemical-GSM2183909.end2.fastq183.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.183
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq184.gz Chemical-GSM2183909.end2.fastq184.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.184
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq185.gz Chemical-GSM2183909.end2.fastq185.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.185
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq186.gz Chemical-GSM2183909.end2.fastq186.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.186
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq187.gz Chemical-GSM2183909.end2.fastq187.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.187
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq188.gz Chemical-GSM2183909.end2.fastq188.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.188
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq189.gz Chemical-GSM2183909.end2.fastq189.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.189
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq18.gz Chemical-GSM2183909.end2.fastq18.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.18
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq190.gz Chemical-GSM2183909.end2.fastq190.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.190
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq191.gz Chemical-GSM2183909.end2.fastq191.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.191
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq192.gz Chemical-GSM2183909.end2.fastq192.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.192
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq193.gz Chemical-GSM2183909.end2.fastq193.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.193
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq194.gz Chemical-GSM2183909.end2.fastq194.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.194
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq195.gz Chemical-GSM2183909.end2.fastq195.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.195
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq196.gz Chemical-GSM2183909.end2.fastq196.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.196
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq197.gz Chemical-GSM2183909.end2.fastq197.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.197
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq198.gz Chemical-GSM2183909.end2.fastq198.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.198
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq199.gz Chemical-GSM2183909.end2.fastq199.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.199
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq19.gz Chemical-GSM2183909.end2.fastq19.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.19
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq1.gz Chemical-GSM2183909.end2.fastq1.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.1
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq200.gz Chemical-GSM2183909.end2.fastq200.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.200
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq201.gz Chemical-GSM2183909.end2.fastq201.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.201
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq202.gz Chemical-GSM2183909.end2.fastq202.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.202
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq203.gz Chemical-GSM2183909.end2.fastq203.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.203
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq204.gz Chemical-GSM2183909.end2.fastq204.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.204
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq205.gz Chemical-GSM2183909.end2.fastq205.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.205
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq206.gz Chemical-GSM2183909.end2.fastq206.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.206
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq207.gz Chemical-GSM2183909.end2.fastq207.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.207
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq208.gz Chemical-GSM2183909.end2.fastq208.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.208
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq209.gz Chemical-GSM2183909.end2.fastq209.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.209
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq20.gz Chemical-GSM2183909.end2.fastq20.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.20
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq210.gz Chemical-GSM2183909.end2.fastq210.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.210
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq211.gz Chemical-GSM2183909.end2.fastq211.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.211
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq212.gz Chemical-GSM2183909.end2.fastq212.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.212
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq213.gz Chemical-GSM2183909.end2.fastq213.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.213
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq214.gz Chemical-GSM2183909.end2.fastq214.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.214
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq215.gz Chemical-GSM2183909.end2.fastq215.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.215
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq216.gz Chemical-GSM2183909.end2.fastq216.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.216
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq217.gz Chemical-GSM2183909.end2.fastq217.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.217
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq218.gz Chemical-GSM2183909.end2.fastq218.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.218
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq219.gz Chemical-GSM2183909.end2.fastq219.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.219
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq21.gz Chemical-GSM2183909.end2.fastq21.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.21
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq220.gz Chemical-GSM2183909.end2.fastq220.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.220
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq221.gz Chemical-GSM2183909.end2.fastq221.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.221
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq222.gz Chemical-GSM2183909.end2.fastq222.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.222
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq223.gz Chemical-GSM2183909.end2.fastq223.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.223
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq224.gz Chemical-GSM2183909.end2.fastq224.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.224
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq225.gz Chemical-GSM2183909.end2.fastq225.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.225
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq226.gz Chemical-GSM2183909.end2.fastq226.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.226
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq227.gz Chemical-GSM2183909.end2.fastq227.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.227
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq228.gz Chemical-GSM2183909.end2.fastq228.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.228
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq229.gz Chemical-GSM2183909.end2.fastq229.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.229
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq22.gz Chemical-GSM2183909.end2.fastq22.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.22
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq230.gz Chemical-GSM2183909.end2.fastq230.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.230
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq231.gz Chemical-GSM2183909.end2.fastq231.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.231
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq232.gz Chemical-GSM2183909.end2.fastq232.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.232
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq233.gz Chemical-GSM2183909.end2.fastq233.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.233
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq234.gz Chemical-GSM2183909.end2.fastq234.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.234
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq235.gz Chemical-GSM2183909.end2.fastq235.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.235
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq236.gz Chemical-GSM2183909.end2.fastq236.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.236
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq237.gz Chemical-GSM2183909.end2.fastq237.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.237
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq238.gz Chemical-GSM2183909.end2.fastq238.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.238
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq239.gz Chemical-GSM2183909.end2.fastq239.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.239
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq23.gz Chemical-GSM2183909.end2.fastq23.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.23
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq240.gz Chemical-GSM2183909.end2.fastq240.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.240
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq241.gz Chemical-GSM2183909.end2.fastq241.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.241
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq242.gz Chemical-GSM2183909.end2.fastq242.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.242
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq243.gz Chemical-GSM2183909.end2.fastq243.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.243
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq244.gz Chemical-GSM2183909.end2.fastq244.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.244
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq245.gz Chemical-GSM2183909.end2.fastq245.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.245
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq246.gz Chemical-GSM2183909.end2.fastq246.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.246
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq247.gz Chemical-GSM2183909.end2.fastq247.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.247
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq248.gz Chemical-GSM2183909.end2.fastq248.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.248
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq249.gz Chemical-GSM2183909.end2.fastq249.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.249
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq24.gz Chemical-GSM2183909.end2.fastq24.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.24
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq250.gz Chemical-GSM2183909.end2.fastq250.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.250
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq251.gz Chemical-GSM2183909.end2.fastq251.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.251
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq252.gz Chemical-GSM2183909.end2.fastq252.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.252
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq253.gz Chemical-GSM2183909.end2.fastq253.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.253
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq254.gz Chemical-GSM2183909.end2.fastq254.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.254
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq255.gz Chemical-GSM2183909.end2.fastq255.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.255
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq256.gz Chemical-GSM2183909.end2.fastq256.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.256
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq257.gz Chemical-GSM2183909.end2.fastq257.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.257
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq258.gz Chemical-GSM2183909.end2.fastq258.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.258
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq259.gz Chemical-GSM2183909.end2.fastq259.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.259
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq25.gz Chemical-GSM2183909.end2.fastq25.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.25
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq260.gz Chemical-GSM2183909.end2.fastq260.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.260
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq261.gz Chemical-GSM2183909.end2.fastq261.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.261
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq262.gz Chemical-GSM2183909.end2.fastq262.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.262
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq263.gz Chemical-GSM2183909.end2.fastq263.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.263
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq264.gz Chemical-GSM2183909.end2.fastq264.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.264
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq265.gz Chemical-GSM2183909.end2.fastq265.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.265
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq266.gz Chemical-GSM2183909.end2.fastq266.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.266
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq267.gz Chemical-GSM2183909.end2.fastq267.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.267
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq268.gz Chemical-GSM2183909.end2.fastq268.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.268
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq269.gz Chemical-GSM2183909.end2.fastq269.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.269
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq26.gz Chemical-GSM2183909.end2.fastq26.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.26
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq270.gz Chemical-GSM2183909.end2.fastq270.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.270
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq271.gz Chemical-GSM2183909.end2.fastq271.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.271
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq272.gz Chemical-GSM2183909.end2.fastq272.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.272
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq273.gz Chemical-GSM2183909.end2.fastq273.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.273
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq274.gz Chemical-GSM2183909.end2.fastq274.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.274
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq275.gz Chemical-GSM2183909.end2.fastq275.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.275
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq276.gz Chemical-GSM2183909.end2.fastq276.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.276
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq277.gz Chemical-GSM2183909.end2.fastq277.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.277
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq278.gz Chemical-GSM2183909.end2.fastq278.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.278
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq279.gz Chemical-GSM2183909.end2.fastq279.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.279
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq27.gz Chemical-GSM2183909.end2.fastq27.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.27
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq280.gz Chemical-GSM2183909.end2.fastq280.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.280
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq281.gz Chemical-GSM2183909.end2.fastq281.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.281
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq282.gz Chemical-GSM2183909.end2.fastq282.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.282
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq28.gz Chemical-GSM2183909.end2.fastq28.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.28
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq29.gz Chemical-GSM2183909.end2.fastq29.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.29
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq2.gz Chemical-GSM2183909.end2.fastq2.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.2
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq30.gz Chemical-GSM2183909.end2.fastq30.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.30
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq31.gz Chemical-GSM2183909.end2.fastq31.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.31
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq32.gz Chemical-GSM2183909.end2.fastq32.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.32
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq33.gz Chemical-GSM2183909.end2.fastq33.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.33
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq34.gz Chemical-GSM2183909.end2.fastq34.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.34
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq35.gz Chemical-GSM2183909.end2.fastq35.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.35
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq36.gz Chemical-GSM2183909.end2.fastq36.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.36
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq37.gz Chemical-GSM2183909.end2.fastq37.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.37
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq38.gz Chemical-GSM2183909.end2.fastq38.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.38
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq39.gz Chemical-GSM2183909.end2.fastq39.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.39
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq3.gz Chemical-GSM2183909.end2.fastq3.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.3
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq40.gz Chemical-GSM2183909.end2.fastq40.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.40
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq41.gz Chemical-GSM2183909.end2.fastq41.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.41
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq42.gz Chemical-GSM2183909.end2.fastq42.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.42
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq43.gz Chemical-GSM2183909.end2.fastq43.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.43
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq44.gz Chemical-GSM2183909.end2.fastq44.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.44
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq45.gz Chemical-GSM2183909.end2.fastq45.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.45
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq46.gz Chemical-GSM2183909.end2.fastq46.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.46
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq47.gz Chemical-GSM2183909.end2.fastq47.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.47
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq48.gz Chemical-GSM2183909.end2.fastq48.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.48
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq49.gz Chemical-GSM2183909.end2.fastq49.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.49
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq4.gz Chemical-GSM2183909.end2.fastq4.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.4
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq50.gz Chemical-GSM2183909.end2.fastq50.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.50
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq51.gz Chemical-GSM2183909.end2.fastq51.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.51
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq52.gz Chemical-GSM2183909.end2.fastq52.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.52
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq53.gz Chemical-GSM2183909.end2.fastq53.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.53
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq54.gz Chemical-GSM2183909.end2.fastq54.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.54
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq55.gz Chemical-GSM2183909.end2.fastq55.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.55
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq56.gz Chemical-GSM2183909.end2.fastq56.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.56
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq57.gz Chemical-GSM2183909.end2.fastq57.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.57
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq58.gz Chemical-GSM2183909.end2.fastq58.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.58
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq59.gz Chemical-GSM2183909.end2.fastq59.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.59
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq5.gz Chemical-GSM2183909.end2.fastq5.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.5
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq60.gz Chemical-GSM2183909.end2.fastq60.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.60
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq61.gz Chemical-GSM2183909.end2.fastq61.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.61
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq62.gz Chemical-GSM2183909.end2.fastq62.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.62
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq63.gz Chemical-GSM2183909.end2.fastq63.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.63
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq64.gz Chemical-GSM2183909.end2.fastq64.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.64
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq65.gz Chemical-GSM2183909.end2.fastq65.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.65
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq66.gz Chemical-GSM2183909.end2.fastq66.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.66
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq67.gz Chemical-GSM2183909.end2.fastq67.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.67
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq68.gz Chemical-GSM2183909.end2.fastq68.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.68
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq69.gz Chemical-GSM2183909.end2.fastq69.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.69
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq6.gz Chemical-GSM2183909.end2.fastq6.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.6
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq70.gz Chemical-GSM2183909.end2.fastq70.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.70
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq71.gz Chemical-GSM2183909.end2.fastq71.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.71
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq72.gz Chemical-GSM2183909.end2.fastq72.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.72
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq73.gz Chemical-GSM2183909.end2.fastq73.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.73
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq74.gz Chemical-GSM2183909.end2.fastq74.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.74
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq75.gz Chemical-GSM2183909.end2.fastq75.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.75
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq76.gz Chemical-GSM2183909.end2.fastq76.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.76
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq77.gz Chemical-GSM2183909.end2.fastq77.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.77
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq78.gz Chemical-GSM2183909.end2.fastq78.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.78
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq79.gz Chemical-GSM2183909.end2.fastq79.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.79
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq7.gz Chemical-GSM2183909.end2.fastq7.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.7
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq80.gz Chemical-GSM2183909.end2.fastq80.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.80
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq81.gz Chemical-GSM2183909.end2.fastq81.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.81
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq82.gz Chemical-GSM2183909.end2.fastq82.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.82
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq83.gz Chemical-GSM2183909.end2.fastq83.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.83
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq84.gz Chemical-GSM2183909.end2.fastq84.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.84
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq85.gz Chemical-GSM2183909.end2.fastq85.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.85
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq86.gz Chemical-GSM2183909.end2.fastq86.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.86
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq87.gz Chemical-GSM2183909.end2.fastq87.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.87
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq88.gz Chemical-GSM2183909.end2.fastq88.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.88
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq89.gz Chemical-GSM2183909.end2.fastq89.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.89
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq8.gz Chemical-GSM2183909.end2.fastq8.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.8
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq90.gz Chemical-GSM2183909.end2.fastq90.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.90
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq91.gz Chemical-GSM2183909.end2.fastq91.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.91
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq92.gz Chemical-GSM2183909.end2.fastq92.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.92
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq93.gz Chemical-GSM2183909.end2.fastq93.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.93
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq94.gz Chemical-GSM2183909.end2.fastq94.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.94
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq95.gz Chemical-GSM2183909.end2.fastq95.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.95
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq96.gz Chemical-GSM2183909.end2.fastq96.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.96
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq97.gz Chemical-GSM2183909.end2.fastq97.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.97
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq98.gz Chemical-GSM2183909.end2.fastq98.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.98
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq99.gz Chemical-GSM2183909.end2.fastq99.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.99
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq9.gz Chemical-GSM2183909.end2.fastq9.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x36mers.mm10.unique.9
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq0.gz Chemical-GSM2183909.end2.fastq0.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.0
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq100.gz Chemical-GSM2183909.end2.fastq100.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.100
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq101.gz Chemical-GSM2183909.end2.fastq101.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.101
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq102.gz Chemical-GSM2183909.end2.fastq102.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.102
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq103.gz Chemical-GSM2183909.end2.fastq103.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.103
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq104.gz Chemical-GSM2183909.end2.fastq104.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.104
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq105.gz Chemical-GSM2183909.end2.fastq105.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.105
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq106.gz Chemical-GSM2183909.end2.fastq106.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.106
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq107.gz Chemical-GSM2183909.end2.fastq107.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.107
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq108.gz Chemical-GSM2183909.end2.fastq108.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.108
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq109.gz Chemical-GSM2183909.end2.fastq109.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.109
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq10.gz Chemical-GSM2183909.end2.fastq10.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.10
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq110.gz Chemical-GSM2183909.end2.fastq110.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.110
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq111.gz Chemical-GSM2183909.end2.fastq111.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.111
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq112.gz Chemical-GSM2183909.end2.fastq112.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.112
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq113.gz Chemical-GSM2183909.end2.fastq113.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.113
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq114.gz Chemical-GSM2183909.end2.fastq114.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.114
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq115.gz Chemical-GSM2183909.end2.fastq115.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.115
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq116.gz Chemical-GSM2183909.end2.fastq116.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.116
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq117.gz Chemical-GSM2183909.end2.fastq117.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.117
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq118.gz Chemical-GSM2183909.end2.fastq118.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.118
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq119.gz Chemical-GSM2183909.end2.fastq119.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.119
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq11.gz Chemical-GSM2183909.end2.fastq11.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.11
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq120.gz Chemical-GSM2183909.end2.fastq120.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.120
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq121.gz Chemical-GSM2183909.end2.fastq121.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.121
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq122.gz Chemical-GSM2183909.end2.fastq122.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.122
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq123.gz Chemical-GSM2183909.end2.fastq123.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.123
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq124.gz Chemical-GSM2183909.end2.fastq124.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.124
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq125.gz Chemical-GSM2183909.end2.fastq125.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.125
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq126.gz Chemical-GSM2183909.end2.fastq126.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.126
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq127.gz Chemical-GSM2183909.end2.fastq127.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.127
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq128.gz Chemical-GSM2183909.end2.fastq128.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.128
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq129.gz Chemical-GSM2183909.end2.fastq129.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.129
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq12.gz Chemical-GSM2183909.end2.fastq12.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.12
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq130.gz Chemical-GSM2183909.end2.fastq130.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.130
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq131.gz Chemical-GSM2183909.end2.fastq131.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.131
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq132.gz Chemical-GSM2183909.end2.fastq132.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.132
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq133.gz Chemical-GSM2183909.end2.fastq133.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.133
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq134.gz Chemical-GSM2183909.end2.fastq134.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.134
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq135.gz Chemical-GSM2183909.end2.fastq135.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.135
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq136.gz Chemical-GSM2183909.end2.fastq136.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.136
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq137.gz Chemical-GSM2183909.end2.fastq137.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.137
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq138.gz Chemical-GSM2183909.end2.fastq138.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.138
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq139.gz Chemical-GSM2183909.end2.fastq139.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.139
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq13.gz Chemical-GSM2183909.end2.fastq13.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.13
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq140.gz Chemical-GSM2183909.end2.fastq140.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.140
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq141.gz Chemical-GSM2183909.end2.fastq141.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.141
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq142.gz Chemical-GSM2183909.end2.fastq142.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.142
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq143.gz Chemical-GSM2183909.end2.fastq143.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.143
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq144.gz Chemical-GSM2183909.end2.fastq144.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.144
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq145.gz Chemical-GSM2183909.end2.fastq145.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.145
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq146.gz Chemical-GSM2183909.end2.fastq146.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.146
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq147.gz Chemical-GSM2183909.end2.fastq147.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.147
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq148.gz Chemical-GSM2183909.end2.fastq148.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.148
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq149.gz Chemical-GSM2183909.end2.fastq149.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.149
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq14.gz Chemical-GSM2183909.end2.fastq14.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.14
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq150.gz Chemical-GSM2183909.end2.fastq150.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.150
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq151.gz Chemical-GSM2183909.end2.fastq151.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.151
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq152.gz Chemical-GSM2183909.end2.fastq152.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.152
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq153.gz Chemical-GSM2183909.end2.fastq153.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.153
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq154.gz Chemical-GSM2183909.end2.fastq154.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.154
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq155.gz Chemical-GSM2183909.end2.fastq155.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.155
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq156.gz Chemical-GSM2183909.end2.fastq156.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.156
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq157.gz Chemical-GSM2183909.end2.fastq157.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.157
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq158.gz Chemical-GSM2183909.end2.fastq158.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.158
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq159.gz Chemical-GSM2183909.end2.fastq159.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.159
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq15.gz Chemical-GSM2183909.end2.fastq15.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.15
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq160.gz Chemical-GSM2183909.end2.fastq160.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.160
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq161.gz Chemical-GSM2183909.end2.fastq161.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.161
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq162.gz Chemical-GSM2183909.end2.fastq162.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.162
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq163.gz Chemical-GSM2183909.end2.fastq163.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.163
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq164.gz Chemical-GSM2183909.end2.fastq164.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.164
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq165.gz Chemical-GSM2183909.end2.fastq165.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.165
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq166.gz Chemical-GSM2183909.end2.fastq166.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.166
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq167.gz Chemical-GSM2183909.end2.fastq167.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.167
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq168.gz Chemical-GSM2183909.end2.fastq168.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.168
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq169.gz Chemical-GSM2183909.end2.fastq169.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.169
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq16.gz Chemical-GSM2183909.end2.fastq16.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.16
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq170.gz Chemical-GSM2183909.end2.fastq170.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.170
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq171.gz Chemical-GSM2183909.end2.fastq171.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.171
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq172.gz Chemical-GSM2183909.end2.fastq172.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.172
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq173.gz Chemical-GSM2183909.end2.fastq173.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.173
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq174.gz Chemical-GSM2183909.end2.fastq174.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.174
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq175.gz Chemical-GSM2183909.end2.fastq175.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.175
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq176.gz Chemical-GSM2183909.end2.fastq176.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.176
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq177.gz Chemical-GSM2183909.end2.fastq177.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.177
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq178.gz Chemical-GSM2183909.end2.fastq178.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.178
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq179.gz Chemical-GSM2183909.end2.fastq179.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.179
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq17.gz Chemical-GSM2183909.end2.fastq17.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.17
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq180.gz Chemical-GSM2183909.end2.fastq180.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.180
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq181.gz Chemical-GSM2183909.end2.fastq181.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.181
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq182.gz Chemical-GSM2183909.end2.fastq182.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.182
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq183.gz Chemical-GSM2183909.end2.fastq183.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.183
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq184.gz Chemical-GSM2183909.end2.fastq184.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.184
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq185.gz Chemical-GSM2183909.end2.fastq185.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.185
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq186.gz Chemical-GSM2183909.end2.fastq186.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.186
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq187.gz Chemical-GSM2183909.end2.fastq187.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.187
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq188.gz Chemical-GSM2183909.end2.fastq188.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.188
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq189.gz Chemical-GSM2183909.end2.fastq189.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.189
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq18.gz Chemical-GSM2183909.end2.fastq18.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.18
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq190.gz Chemical-GSM2183909.end2.fastq190.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.190
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq191.gz Chemical-GSM2183909.end2.fastq191.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.191
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq192.gz Chemical-GSM2183909.end2.fastq192.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.192
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq193.gz Chemical-GSM2183909.end2.fastq193.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.193
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq194.gz Chemical-GSM2183909.end2.fastq194.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.194
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq195.gz Chemical-GSM2183909.end2.fastq195.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.195
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq196.gz Chemical-GSM2183909.end2.fastq196.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.196
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq197.gz Chemical-GSM2183909.end2.fastq197.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.197
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq198.gz Chemical-GSM2183909.end2.fastq198.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.198
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq199.gz Chemical-GSM2183909.end2.fastq199.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.199
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq19.gz Chemical-GSM2183909.end2.fastq19.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.19
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq1.gz Chemical-GSM2183909.end2.fastq1.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.1
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq200.gz Chemical-GSM2183909.end2.fastq200.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.200
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq201.gz Chemical-GSM2183909.end2.fastq201.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.201
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq202.gz Chemical-GSM2183909.end2.fastq202.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.202
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq203.gz Chemical-GSM2183909.end2.fastq203.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.203
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq204.gz Chemical-GSM2183909.end2.fastq204.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.204
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq205.gz Chemical-GSM2183909.end2.fastq205.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.205
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq206.gz Chemical-GSM2183909.end2.fastq206.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.206
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq207.gz Chemical-GSM2183909.end2.fastq207.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.207
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq208.gz Chemical-GSM2183909.end2.fastq208.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.208
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq209.gz Chemical-GSM2183909.end2.fastq209.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.209
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq20.gz Chemical-GSM2183909.end2.fastq20.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.20
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq210.gz Chemical-GSM2183909.end2.fastq210.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.210
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq211.gz Chemical-GSM2183909.end2.fastq211.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.211
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq212.gz Chemical-GSM2183909.end2.fastq212.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.212
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq213.gz Chemical-GSM2183909.end2.fastq213.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.213
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq214.gz Chemical-GSM2183909.end2.fastq214.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.214
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq215.gz Chemical-GSM2183909.end2.fastq215.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.215
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq216.gz Chemical-GSM2183909.end2.fastq216.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.216
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq217.gz Chemical-GSM2183909.end2.fastq217.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.217
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq218.gz Chemical-GSM2183909.end2.fastq218.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.218
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq219.gz Chemical-GSM2183909.end2.fastq219.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.219
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq21.gz Chemical-GSM2183909.end2.fastq21.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.21
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq220.gz Chemical-GSM2183909.end2.fastq220.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.220
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq221.gz Chemical-GSM2183909.end2.fastq221.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.221
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq222.gz Chemical-GSM2183909.end2.fastq222.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.222
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq223.gz Chemical-GSM2183909.end2.fastq223.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.223
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq224.gz Chemical-GSM2183909.end2.fastq224.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.224
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq225.gz Chemical-GSM2183909.end2.fastq225.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.225
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq226.gz Chemical-GSM2183909.end2.fastq226.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.226
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq227.gz Chemical-GSM2183909.end2.fastq227.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.227
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq228.gz Chemical-GSM2183909.end2.fastq228.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.228
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq229.gz Chemical-GSM2183909.end2.fastq229.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.229
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq22.gz Chemical-GSM2183909.end2.fastq22.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.22
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq230.gz Chemical-GSM2183909.end2.fastq230.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.230
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq231.gz Chemical-GSM2183909.end2.fastq231.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.231
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq232.gz Chemical-GSM2183909.end2.fastq232.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.232
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq233.gz Chemical-GSM2183909.end2.fastq233.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.233
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq234.gz Chemical-GSM2183909.end2.fastq234.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.234
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq235.gz Chemical-GSM2183909.end2.fastq235.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.235
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq236.gz Chemical-GSM2183909.end2.fastq236.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.236
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq237.gz Chemical-GSM2183909.end2.fastq237.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.237
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq238.gz Chemical-GSM2183909.end2.fastq238.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.238
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq239.gz Chemical-GSM2183909.end2.fastq239.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.239
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq23.gz Chemical-GSM2183909.end2.fastq23.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.23
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq240.gz Chemical-GSM2183909.end2.fastq240.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.240
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq241.gz Chemical-GSM2183909.end2.fastq241.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.241
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq242.gz Chemical-GSM2183909.end2.fastq242.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.242
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq243.gz Chemical-GSM2183909.end2.fastq243.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.243
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq244.gz Chemical-GSM2183909.end2.fastq244.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.244
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq245.gz Chemical-GSM2183909.end2.fastq245.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.245
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq246.gz Chemical-GSM2183909.end2.fastq246.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.246
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq247.gz Chemical-GSM2183909.end2.fastq247.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.247
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq248.gz Chemical-GSM2183909.end2.fastq248.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.248
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq249.gz Chemical-GSM2183909.end2.fastq249.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.249
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq24.gz Chemical-GSM2183909.end2.fastq24.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.24
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq250.gz Chemical-GSM2183909.end2.fastq250.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.250
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq251.gz Chemical-GSM2183909.end2.fastq251.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.251
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq252.gz Chemical-GSM2183909.end2.fastq252.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.252
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq253.gz Chemical-GSM2183909.end2.fastq253.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.253
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq254.gz Chemical-GSM2183909.end2.fastq254.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.254
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq255.gz Chemical-GSM2183909.end2.fastq255.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.255
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq256.gz Chemical-GSM2183909.end2.fastq256.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.256
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq257.gz Chemical-GSM2183909.end2.fastq257.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.257
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq258.gz Chemical-GSM2183909.end2.fastq258.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.258
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq259.gz Chemical-GSM2183909.end2.fastq259.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.259
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq25.gz Chemical-GSM2183909.end2.fastq25.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.25
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq260.gz Chemical-GSM2183909.end2.fastq260.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.260
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq261.gz Chemical-GSM2183909.end2.fastq261.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.261
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq262.gz Chemical-GSM2183909.end2.fastq262.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.262
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq263.gz Chemical-GSM2183909.end2.fastq263.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.263
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq264.gz Chemical-GSM2183909.end2.fastq264.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.264
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq265.gz Chemical-GSM2183909.end2.fastq265.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.265
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq266.gz Chemical-GSM2183909.end2.fastq266.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.266
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq267.gz Chemical-GSM2183909.end2.fastq267.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.267
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq268.gz Chemical-GSM2183909.end2.fastq268.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.268
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq269.gz Chemical-GSM2183909.end2.fastq269.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.269
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq26.gz Chemical-GSM2183909.end2.fastq26.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.26
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq270.gz Chemical-GSM2183909.end2.fastq270.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.270
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq271.gz Chemical-GSM2183909.end2.fastq271.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.271
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq272.gz Chemical-GSM2183909.end2.fastq272.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.272
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq273.gz Chemical-GSM2183909.end2.fastq273.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.273
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq274.gz Chemical-GSM2183909.end2.fastq274.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.274
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq275.gz Chemical-GSM2183909.end2.fastq275.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.275
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq276.gz Chemical-GSM2183909.end2.fastq276.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.276
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq277.gz Chemical-GSM2183909.end2.fastq277.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.277
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq278.gz Chemical-GSM2183909.end2.fastq278.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.278
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq279.gz Chemical-GSM2183909.end2.fastq279.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.279
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq27.gz Chemical-GSM2183909.end2.fastq27.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.27
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq280.gz Chemical-GSM2183909.end2.fastq280.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.280
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq281.gz Chemical-GSM2183909.end2.fastq281.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.281
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq282.gz Chemical-GSM2183909.end2.fastq282.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.282
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq28.gz Chemical-GSM2183909.end2.fastq28.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.28
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq29.gz Chemical-GSM2183909.end2.fastq29.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.29
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq2.gz Chemical-GSM2183909.end2.fastq2.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.2
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq30.gz Chemical-GSM2183909.end2.fastq30.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.30
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq31.gz Chemical-GSM2183909.end2.fastq31.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.31
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq32.gz Chemical-GSM2183909.end2.fastq32.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.32
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq33.gz Chemical-GSM2183909.end2.fastq33.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.33
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq34.gz Chemical-GSM2183909.end2.fastq34.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.34
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq35.gz Chemical-GSM2183909.end2.fastq35.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.35
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq36.gz Chemical-GSM2183909.end2.fastq36.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.36
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq37.gz Chemical-GSM2183909.end2.fastq37.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.37
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq38.gz Chemical-GSM2183909.end2.fastq38.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.38
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq39.gz Chemical-GSM2183909.end2.fastq39.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.39
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq3.gz Chemical-GSM2183909.end2.fastq3.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.3
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq40.gz Chemical-GSM2183909.end2.fastq40.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.40
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq41.gz Chemical-GSM2183909.end2.fastq41.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.41
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq42.gz Chemical-GSM2183909.end2.fastq42.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.42
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq43.gz Chemical-GSM2183909.end2.fastq43.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.43
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq44.gz Chemical-GSM2183909.end2.fastq44.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.44
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq45.gz Chemical-GSM2183909.end2.fastq45.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.45
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq46.gz Chemical-GSM2183909.end2.fastq46.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.46
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq47.gz Chemical-GSM2183909.end2.fastq47.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.47
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq48.gz Chemical-GSM2183909.end2.fastq48.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.48
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq49.gz Chemical-GSM2183909.end2.fastq49.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.49
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq4.gz Chemical-GSM2183909.end2.fastq4.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.4
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq50.gz Chemical-GSM2183909.end2.fastq50.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.50
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq51.gz Chemical-GSM2183909.end2.fastq51.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.51
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq52.gz Chemical-GSM2183909.end2.fastq52.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.52
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq53.gz Chemical-GSM2183909.end2.fastq53.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.53
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq54.gz Chemical-GSM2183909.end2.fastq54.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.54
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq55.gz Chemical-GSM2183909.end2.fastq55.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.55
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq56.gz Chemical-GSM2183909.end2.fastq56.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.56
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq57.gz Chemical-GSM2183909.end2.fastq57.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.57
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq58.gz Chemical-GSM2183909.end2.fastq58.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.58
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq59.gz Chemical-GSM2183909.end2.fastq59.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.59
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq5.gz Chemical-GSM2183909.end2.fastq5.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.5
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq60.gz Chemical-GSM2183909.end2.fastq60.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.60
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq61.gz Chemical-GSM2183909.end2.fastq61.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.61
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq62.gz Chemical-GSM2183909.end2.fastq62.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.62
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq63.gz Chemical-GSM2183909.end2.fastq63.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.63
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq64.gz Chemical-GSM2183909.end2.fastq64.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.64
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq65.gz Chemical-GSM2183909.end2.fastq65.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.65
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq66.gz Chemical-GSM2183909.end2.fastq66.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.66
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq67.gz Chemical-GSM2183909.end2.fastq67.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.67
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq68.gz Chemical-GSM2183909.end2.fastq68.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.68
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq69.gz Chemical-GSM2183909.end2.fastq69.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.69
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq6.gz Chemical-GSM2183909.end2.fastq6.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.6
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq70.gz Chemical-GSM2183909.end2.fastq70.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.70
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq71.gz Chemical-GSM2183909.end2.fastq71.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.71
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq72.gz Chemical-GSM2183909.end2.fastq72.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.72
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq73.gz Chemical-GSM2183909.end2.fastq73.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.73
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq74.gz Chemical-GSM2183909.end2.fastq74.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.74
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq75.gz Chemical-GSM2183909.end2.fastq75.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.75
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq76.gz Chemical-GSM2183909.end2.fastq76.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.76
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq77.gz Chemical-GSM2183909.end2.fastq77.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.77
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq78.gz Chemical-GSM2183909.end2.fastq78.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.78
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq79.gz Chemical-GSM2183909.end2.fastq79.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.79
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq7.gz Chemical-GSM2183909.end2.fastq7.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.7
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq80.gz Chemical-GSM2183909.end2.fastq80.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.80
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq81.gz Chemical-GSM2183909.end2.fastq81.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.81
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq82.gz Chemical-GSM2183909.end2.fastq82.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.82
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq83.gz Chemical-GSM2183909.end2.fastq83.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.83
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq84.gz Chemical-GSM2183909.end2.fastq84.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.84
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq85.gz Chemical-GSM2183909.end2.fastq85.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.85
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq86.gz Chemical-GSM2183909.end2.fastq86.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.86
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq87.gz Chemical-GSM2183909.end2.fastq87.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.87
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq88.gz Chemical-GSM2183909.end2.fastq88.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.88
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq89.gz Chemical-GSM2183909.end2.fastq89.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.89
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq8.gz Chemical-GSM2183909.end2.fastq8.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.8
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq90.gz Chemical-GSM2183909.end2.fastq90.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.90
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq91.gz Chemical-GSM2183909.end2.fastq91.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.91
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq92.gz Chemical-GSM2183909.end2.fastq92.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.92
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq93.gz Chemical-GSM2183909.end2.fastq93.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.93
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq94.gz Chemical-GSM2183909.end2.fastq94.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.94
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq95.gz Chemical-GSM2183909.end2.fastq95.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.95
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq96.gz Chemical-GSM2183909.end2.fastq96.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.96
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq97.gz Chemical-GSM2183909.end2.fastq97.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.97
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq98.gz Chemical-GSM2183909.end2.fastq98.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.98
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq99.gz Chemical-GSM2183909.end2.fastq99.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.99
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chemical-GSM2183909.end1.fastq9.gz Chemical-GSM2183909.end2.fastq9.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 60 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chemical-GSM2183909.2x50mers.mm10.unique.9