python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC61_rep1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1 -p 20 -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC61_rep1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC61_rep1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1 -p 20 -v 1 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC61_rep1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC61_rep2.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1 -p 20 -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC61_rep2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC61_rep2.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1 -p 20 -v 1 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC61_rep2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py halo_nac_r1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1 -p 20 -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - halo_nac_r1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py halo_nac_r1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1 -p 20 -v 1 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - halo_nac_r1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py halo_nac_r2.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1 -p 20 -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - halo_nac_r2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py halo_nac_r2.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1 -p 20 -v 1 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Vitis_vinifera-ASM3070453v1/bowtie-indexes/Vitis_vinifera-ASM3070453v1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - halo_nac_r2.SE.a