python ~/code/PEFastqToTabDelimited.py L427_S1_L001_R1_001.fastq.gz L427_S1_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L427-YPD-WT-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L428_S2_L001_R1_001.fastq.gz L428_S2_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L428-YPD-WT-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L429_S3_L001_R1_001.fastq.gz L429_S3_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L429-YPD-asf1-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L430_S4_L001_R1_001.fastq.gz L430_S4_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L430-YPD-asf1-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L431_S5_L001_R1_001.fastq.gz L431_S5_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L431-YPD-rtt109-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L432_S6_L001_R1_001.fastq.gz L432_S6_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L432-YPD-rtt109-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L433_S7_L001_R1_001.fastq.gz L433_S7_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L433-YPGE-WT-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L434_S8_L001_R1_001.fastq.gz L434_S8_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L434-YPGE-WT-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L435_S9_L001_R1_001.fastq.gz L435_S9_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L435-YPGE-asf1-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L436_S10_L001_R1_001.fastq.gz L436_S10_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L436-YPGE-asf1-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L437_S11_L001_R1_001.fastq.gz L437_S11_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L437-YPGE-spt10-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L438_S12_L001_R1_001.fastq.gz L438_S12_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L438-YPGE-spt10-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L439_S13_L001_R1_001.fastq.gz L439_S13_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L439-YPD-spt10-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L440_S14_L001_R1_001.fastq.gz L440_S14_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L440-YPD-spt10-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L441_S15_L001_R1_001.fastq.gz L441_S15_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L441-YPD-rlf2-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L442_S16_L001_R1_001.fastq.gz L442_S16_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L442-YPD-rlf2-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L443_S17_L001_R1_001.fastq.gz L443_S17_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L443-YPD-hir1-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L444_S18_L001_R1_001.fastq.gz L444_S18_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L444-YPD-hir1-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L445_S19_L001_R1_001.fastq.gz L445_S19_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L445-YPD-hir2-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L446_S20_L001_R1_001.fastq.gz L446_S20_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L446-YPD-hir2-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L447_S21_L001_R1_001.fastq.gz L447_S21_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L447-YPD-hir3-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L448_S22_L001_R1_001.fastq.gz L448_S22_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L448-YPD-hir3-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L449_S23_L001_R1_001.fastq.gz L449_S23_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L449-YPD-hpc2-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L450_S24_L001_R1_001.fastq.gz L450_S24_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L450-YPD-hpc2-rep2.2x36mers.unique