python ~/code/PEFastqToTabDelimited.py L524-rDNA-146.end1.fastq.gz L524-rDNA-146.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 - L524-rDNA-146.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L525-rDNA-147.end1.fastq.gz L525-rDNA-147.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -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 - L525-rDNA-147.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L524-rDNA-146.end1.fastq.gz L524-rDNA-146.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -v 2 -a -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 - L524-rDNA-146.2x36mers.a
python ~/code/PEFastqToTabDelimited.py L525-rDNA-147.end1.fastq.gz L525-rDNA-147.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -v 2 -a -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 - L525-rDNA-147.2x36mers.a