python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L08_S1_L001_R1_001.fastq.gz,L08_S1_L002_R1_001.fastq.gz,L08_S1_L003_R1_001.fastq.gz,L08_S1_L004_R1_001.fastq.gz,L08_SM_L001_R1_001.fastq.gz L08_S1_L001_R2_001.fastq.gz,L08_S1_L002_R2_001.fastq.gz,L08_S1_L003_R2_001.fastq.gz,L08_S1_L004_R2_001.fastq.gz,L08_SM_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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome -p 8 -v 2 -k 2 -m 1 -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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L09_S2_L001_R1_001.fastq.gz,L09_S2_L002_R1_001.fastq.gz,L09_S2_L003_R1_001.fastq.gz,L09_S2_L004_R1_001.fastq.gz L09_S2_L001_R2_001.fastq.gz,L09_S2_L002_R2_001.fastq.gz,L09_S2_L003_R2_001.fastq.gz,L09_S2_L004_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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome -p 8 -v 2 -k 2 -m 1 -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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L09_Symbiodinium_minutum_SSb01_spheroplast_5_min_ATAC.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L39_S6_L001_R1_001.fastq.gz,L39_S6_L002_R1_001.fastq.gz,L39_S6_L003_R1_001.fastq.gz,L39_S6_L004_R1_001.fastq.gz L39_S6_L001_R2_001.fastq.gz,L39_S6_L002_R2_001.fastq.gz,L39_S6_L003_R2_001.fastq.gz,L39_S6_L004_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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome -p 8 -v 2 -k 2 -m 1 -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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L39_Symbiodinium_minutum_SSb01_Input_3_min.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L40_S7_L001_R1_001.fastq.gz,L40_S7_L002_R1_001.fastq.gz,L40_S7_L003_R1_001.fastq.gz,L40_S7_L004_R1_001.fastq.gz L40_S7_L001_R2_001.fastq.gz,L40_S7_L002_R2_001.fastq.gz,L40_S7_L003_R2_001.fastq.gz,L40_S7_L004_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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome -p 8 -v 2 -k 2 -m 1 -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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L40_Symbiodinium_minutum_SSb01_Input_9_min.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L41_S8_L001_R1_001.fastq.gz,L41_S8_L002_R1_001.fastq.gz,L41_S8_L003_R1_001.fastq.gz,L41_S8_L004_R1_001.fastq.gz L41_S8_L001_R2_001.fastq.gz,L41_S8_L002_R2_001.fastq.gz,L41_S8_L003_R2_001.fastq.gz,L41_S8_L004_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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome -p 8 -v 2 -k 2 -m 1 -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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L41_Symbiodinium_minutum_SSb01_Input_12_min.2x36mers.unique
zcat L39_S6_L001_R1_001.fastq.gz L39_S6_L002_R1_001.fastq.gz L39_S6_L003_R1_001.fastq.gz L39_S6_L004_R1_001.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/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-0.1.18/samtools sort - L39_Symbiodinium_minutum_SSb01_Input_3_min.1x36mers.unique
zcat L40_S7_L001_R1_001.fastq.gz L40_S7_L002_R1_001.fastq.gz L40_S7_L003_R1_001.fastq.gz L40_S7_L004_R1_001.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/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-0.1.18/samtools sort - L40_Symbiodinium_minutum_SSb01_Input_9_min.1x36mers.unique
zcat L41_S8_L001_R1_001.fastq.gz L41_S8_L002_R1_001.fastq.gz L41_S8_L003_R1_001.fastq.gz L41_S8_L004_R1_001.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/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-0.1.18/samtools sort - L41_Symbiodinium_minutum_SSb01_Input_12_min.1x36mers.unique