python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GBF1.end1.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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GBF1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GBF1.end1.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -k 101 -m 100 -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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GBF1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB115.end1.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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HB115.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB115.end1.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -k 101 -m 100 -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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HB115.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSFTF10.end1.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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HSFTF10.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSFTF10.end1.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -k 101 -m 100 -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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HSFTF10.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NACTF49.end1.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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NACTF49.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NACTF49.end1.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -k 101 -m 100 -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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NACTF49.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NKD1.end1.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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NKD1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NKD1.end1.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -k 101 -m 100 -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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NKD1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NKD2.end1.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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NKD2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NKD2.end1.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -k 101 -m 100 -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/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NKD2.SE.a