python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SSBO1.read1.paired.fastq.gz SSBO1.read2.paired.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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - SSBO1.2x36mers.v0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SSBO1.read1.paired.fastq.gz SSBO1.read2.paired.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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome -p 8 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - SSBO1.2x36mers.v1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SSBO1.read1.paired.fastq.gz SSBO1.read2.paired.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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome -p 8 -v 3 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - SSBO1.2x36mers.v3.unique