python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-09-13-MiSeqRun/MS1-SCD-1_S7_L001_R1_001.fastq.gz 2017-09-13-MiSeqRun/MS1-SCD-1_S7_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WT-MS1-SCD-rep1_S7.2x36mers.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-09-13-MiSeqRun/MS1-SCD-2_S10_L001_R1_001.fastq.gz 2017-09-13-MiSeqRun/MS1-SCD-2_S10_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WT-MS1-SCD-rep2_S10.2x36mers.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-09-13-MiSeqRun/MS1-SCE-1_S1_L001_R1_001.fastq.gz 2017-09-13-MiSeqRun/MS1-SCE-1_S1_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WT-MS1-SCE-rep1_S1.2x36mers.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-09-13-MiSeqRun/MS1-SCE-2_S4_L001_R1_001.fastq.gz 2017-09-13-MiSeqRun/MS1-SCE-2_S4_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WT-MS1-SCE-rep2_S4.2x36mers.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-09-13-MiSeqRun/MS49-SCD-1_S8_L001_R1_001.fastq.gz 2017-09-13-MiSeqRun/MS49-SCD-1_S8_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cln3-MS49-SCD-rep1_S8.2x36mers.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-09-13-MiSeqRun/MS49-SCD-2_S11_L001_R1_001.fastq.gz 2017-09-13-MiSeqRun/MS49-SCD-2_S11_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cln3-MS49-SCD-rep2_S11.2x36mers.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-09-13-MiSeqRun/MS49-SCE-1_S2_L001_R1_001.fastq.gz 2017-09-13-MiSeqRun/MS49-SCE-1_S2_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cln3-MS49-SCE-rep1_S2.2x36mers.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-09-13-MiSeqRun/MS49-SCE-2_S5_L001_R1_001.fastq.gz 2017-09-13-MiSeqRun/MS49-SCE-2_S5_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cln3-MS49-SCE-rep2_S5.2x36mers.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-09-13-MiSeqRun/MS51-SCD-1_S9_L001_R1_001.fastq.gz 2017-09-13-MiSeqRun/MS51-SCD-1_S9_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Whi5-MS51-SCD-rep1_S9.2x36mers.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-09-13-MiSeqRun/MS51-SCD-2_S12_L001_R1_001.fastq.gz 2017-09-13-MiSeqRun/MS51-SCD-2_S12_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Whi5-MS51-SCD-rep2_S12.2x36mers.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-09-13-MiSeqRun/MS51-SCE-1_S3_L001_R1_001.fastq.gz 2017-09-13-MiSeqRun/MS51-SCE-1_S3_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Whi5-MS51-SCE-rep1_S3.2x36mers.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-09-13-MiSeqRun/MS51-SCE-2_S6_L001_R1_001.fastq.gz 2017-09-13-MiSeqRun/MS51-SCE-2_S6_L001_R2_001.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Whi5-MS51-SCE-rep2_S6.2x36mers.a