python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ABI19_B73.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 - ABI19_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ABI19_Mo17.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 - ABI19_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ABI34_B73.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 - ABI34_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ABI34_Mo17.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 - ABI34_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ABI8_B73.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 - ABI8_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ABI8_Mo17.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 - ABI8_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF10_Mo17.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 - ARF10_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF13_Mo17.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 - ARF13_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF14_Mo17.end.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 - ARF14_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF16_Mo17.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 - ARF16_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF18_Mo17.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 - ARF18_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF25_Mo17.end.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 - ARF25_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF27_Mo17.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 - ARF27_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF29_Mo17.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 - ARF29_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF34_Mo17.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 - ARF34_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF35_Mo17.end.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 - ARF35_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF36_Mo17.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 - ARF36_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF39_Mo17.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 - ARF39_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF4_Mo17.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 - ARF4_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF7_Mo17.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 - ARF7_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARR5_B73.end.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 - ARR5_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARR5_Mo17.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 - ARR5_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BAF1_B73.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 - BAF1_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BAF1_Mo17.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 - BAF1_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BAFL12_Mo17.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 - BAFL12_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BAFL3_Mo17.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 - BAFL3_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH106_B73.end.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 - BHLH106_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH106_Mo17.end.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 - BHLH106_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH113_B73.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 - BHLH113_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH113_Mo17.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 - BHLH113_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH125_B73.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 - BHLH125_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH125_Mo17.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 - BHLH125_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH135_B73.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 - BHLH135_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH135_Mo17.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 - BHLH135_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH149_B73.end.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 - BHLH149_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH149_Mo17.end.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 - BHLH149_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH14_B73.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 - BHLH14_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH150_B73.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 - BHLH150_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH150_Mo17.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 - BHLH150_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH168_B73.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 - BHLH168_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH168_Mo17.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 - BHLH168_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH17_B73.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 - BHLH17_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH17_Mo17.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 - BHLH17_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH52_B73.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 - BHLH52_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH52_Mo17.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 - BHLH52_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH57_B73.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 - BHLH57_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH57_Mo17.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 - BHLH57_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH61_B73.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 - BHLH61_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH61_Mo17.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 - BHLH61_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH67_B73.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 - BHLH67_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH67_BA1_Mo17.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 - BHLH67_BA1_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH85_B73.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 - BHLH85_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH85_Mo17.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 - BHLH85_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH91_B73.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 - BHLH91_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH91_Mo17.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 - BHLH91_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH99_B73.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 - BHLH99_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH99_Mo17.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 - BHLH99_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP105_B73.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 - BZIP105_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP105_Mo17.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 - BZIP105_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP106_B73.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 - BZIP106_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP106_Mo17.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 - BZIP106_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP111_B73.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 - BZIP111_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP111_Mo17.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 - BZIP111_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP112_B73.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 - BZIP112_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP112_Mo17.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 - BZIP112_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP115_B73.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 - BZIP115_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP115_Mo17.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 - BZIP115_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP124_B73.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 - BZIP124_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP124_Mo17.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 - BZIP124_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP128_B73.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 - BZIP128_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP128_Mo17.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 - BZIP128_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP12_B73.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 - BZIP12_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP12_Mo17.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 - BZIP12_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP13_B73.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 - BZIP13_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP13_Mo17.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 - BZIP13_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP160_B73.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 - BZIP160_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP160_Mo17.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 - BZIP160_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP1_B73.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 - BZIP1_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP1_Mo17.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 - BZIP1_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP21_B73.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 - BZIP21_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP21_Mo17.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 - BZIP21_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP23_B73.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 - BZIP23_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP23_Mo17.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 - BZIP23_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP25_B73.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 - BZIP25_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP25_Mo17.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 - BZIP25_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP27_B73.end.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 - BZIP27_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP27_Mo17.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 - BZIP27_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP2_B73.end.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 - BZIP2_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP2_Mo17.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 - BZIP2_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP34_B73.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 - BZIP34_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP34_Mo17.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 - BZIP34_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP39_B73.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 - BZIP39_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP39_Mo17.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 - BZIP39_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP40_B73.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 - BZIP40_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP40_Mo17.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 - BZIP40_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP41_B73.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 - BZIP41_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP41_Mo17.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 - BZIP41_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP48_B73.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 - BZIP48_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP48_Mo17.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 - BZIP48_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP52_B73.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 - BZIP52_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP52_Mo17.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 - BZIP52_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP54_B73.end.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 - BZIP54_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP54_Mo17.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 - BZIP54_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP57_Mo17.end.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 - BZIP57_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP58_B73.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 - BZIP58_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP58_Mo17.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 - BZIP58_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP61_B73.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 - BZIP61_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP61_Mo17.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 - BZIP61_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP62_B73.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 - BZIP62_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP62_Mo17.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 - BZIP62_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP68_B73.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 - BZIP68_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP68_Mo17.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 - BZIP68_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP70_B73.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 - BZIP70_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP70_Mo17.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 - BZIP70_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP72_Mo17.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 - BZIP72_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP79_B73.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 - BZIP79_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP79_Mo17.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 - BZIP79_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP84_B73.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 - BZIP84_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP84_Mo17.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 - BZIP84_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP86_B73.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 - BZIP86_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP86_rep1_Mo17.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 - BZIP86_rep1_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP86_rep2_Mo17.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 - BZIP86_rep2_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP87_B73.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 - BZIP87_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP87_Mo17.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 - BZIP87_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP90_B73.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 - BZIP90_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP90_Mo17.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 - BZIP90_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP91_B73.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 - BZIP91_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP91_Mo17.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 - BZIP91_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP92_B73.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 - BZIP92_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP92_Mo17.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 - BZIP92_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP94_B73.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 - BZIP94_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP94_Mo17.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 - BZIP94_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP96_Mo17.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 - BZIP96_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP99_B73.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 - BZIP99_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP99_Mo17.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 - BZIP99_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZR1_B73.end.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 - BZR1_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZR1_Mo17.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 - BZR1_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py CA2P13_CA3P1_CA5P7_B73.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 - CA2P13_CA3P1_CA5P7_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py CA2P13_CA3P1_CA5P7_Mo17.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 - CA2P13_CA3P1_CA5P7_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py CA2P13_CA3P4_CA5P7_B73.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 - CA2P13_CA3P4_CA5P7_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py CA2P13_CA3P4_CA5P7_Mo17.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 - CA2P13_CA3P4_CA5P7_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py CCHH2_B73.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 - CCHH2_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py CCHH2_Mo17.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 - CCHH2_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH113_BHLH125_B73.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 - DD_BHLH113_BHLH125_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH113_BHLH168_B73.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 - DD_BHLH113_BHLH168_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH135_BHLH125_B73.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 - DD_BHLH135_BHLH125_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH135_BHLH168_B73.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 - DD_BHLH135_BHLH168_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH14_BHLH125_B73.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 - DD_BHLH14_BHLH125_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH14_BHLH168_B73.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 - DD_BHLH14_BHLH168_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH150_BHLH125_B73.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 - DD_BHLH150_BHLH125_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH150_BHLH168_B73.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 - DD_BHLH150_BHLH168_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH52_BHLH125_B73.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 - DD_BHLH52_BHLH125_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH52_BHLH168_B73.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 - DD_BHLH52_BHLH168_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH61_BHLH125_B73.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 - DD_BHLH61_BHLH125_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH61_BHLH168_B73.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 - DD_BHLH61_BHLH168_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH67_BHLH125_B73.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 - DD_BHLH67_BHLH125_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH67_BHLH168_B73.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 - DD_BHLH67_BHLH168_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH85_BHLH125_B73.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 - DD_BHLH85_BHLH125_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH85_BHLH125_Mo17.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 - DD_BHLH85_BHLH125_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH85_BHLH168_B73.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 - DD_BHLH85_BHLH168_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH92_BHLH125_B73.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 - DD_BHLH92_BHLH125_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DD_BHLH92_BHLH168_B73.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 - DD_BHLH92_BHLH168_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DOF1_B73.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 - DOF1_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DOF1_Mo17.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 - DOF1_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DOF24_B73.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 - DOF24_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py DOF24_Mo17.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 - DOF24_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB126_B73.end.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 - EREB126_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB126_Mo17.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 - EREB126_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB138_Mo17.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 - EREB138_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB145_B73.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 - EREB145_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB145_Mo17.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 - EREB145_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB149_B73.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 - EREB149_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB149_Mo17.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 - EREB149_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB183_B73.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 - EREB183_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB183_Mo17.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 - EREB183_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB201_B73.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 - EREB201_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB201_Mo17.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 - EREB201_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB24_Mo17.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 - EREB24_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB29_Mo17.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 - EREB29_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB2_B73.end.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 - EREB2_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB2_Mo17.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 - EREB2_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB36_B73.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 - EREB36_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB36_Mo17.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 - EREB36_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB46_B73.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 - EREB46_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB46_Mo17.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 - EREB46_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB49_B73.end.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 - EREB49_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB49_Mo17.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 - EREB49_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB4_B73.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 - EREB4_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB4_Mo17.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 - EREB4_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB53_B73.end.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 - EREB53_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB53_Mo17.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 - EREB53_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB87_B73.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 - EREB87_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB87_Mo17.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 - EREB87_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GATA20_B73.end.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 - GATA20_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GATA20_Mo17.end.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 - GATA20_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GBP10_B73.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 - GBP10_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GBP10_Mo17.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 - GBP10_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GBP11_B73.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 - GBP11_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GBP11_Mo17.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 - GBP11_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GBP4_B73.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 - GBP4_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GBP4_Mo17.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 - GBP4_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK17_B73.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 - GLK17_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK17_Mo17.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 - GLK17_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK20_B73.end.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 - GLK20_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK20_Mo17.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 - GLK20_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK21_B73.end.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 - GLK21_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK21_Mo17.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 - GLK21_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK44_B73.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 - GLK44_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK44_Mo17.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 - GLK44_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK47_B73.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 - GLK47_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK47_Mo17.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 - GLK47_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK48_B73.end.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 - GLK48_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK48_Mo17.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 - GLK48_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK53_B73.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 - GLK53_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK53_Mo17.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 - GLK53_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK56_B73.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 - GLK56_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK56_Mo17.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 - GLK56_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GRF2_B73.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 - GRF2_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GRF2_Mo17.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 - GRF2_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GRF3_B73.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 - GRF3_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GRF3_Mo17.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 - GRF3_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GRF6_B73.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 - GRF6_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GRF6_Mo17.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 - GRF6_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GRF7_B73.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 - GRF7_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GRF7_Mo17.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 - GRF7_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GRF9_B73.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 - GRF9_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GRF9_Mo17.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 - GRF9_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-GST_Mo17.end.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 - HALO-GST_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB102_B73.end.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 - HB102_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB102_Mo17.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 - HB102_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB117_B73.end.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 - HB117_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB117_Mo17.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 - HB117_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB122_B73.end.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 - HB122_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB122_Mo17.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 - HB122_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB125_B73.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 - HB125_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB15_B73.end.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 - HB15_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB15_Mo17.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 - HB15_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB22_B73.end.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 - HB22_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB22_Mo17.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 - HB22_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB54_B73.end.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 - HB54_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB54_Mo17.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 - HB54_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB67_B73.end.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 - HB67_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB67_Mo17.end.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 - HB67_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB68_B73.end.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 - HB68_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB68_Mo17.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 - HB68_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF10_B73.end.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 - HSF10_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF10_Mo17.end.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 - HSF10_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF24_B73.end.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 - HSF24_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF24_Mo17.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 - HSF24_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF25_B73.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 - HSF25_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF25_Mo17.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 - HSF25_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF7_B73.end.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 - HSF7_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF7_Mo17.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 - HSF7_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LBD16_Mo17.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 - LBD16_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LBD19_Mo17.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 - LBD19_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LBD37_B73.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 - LBD37_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LBD37_Mo17.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 - LBD37_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LBD5_Mo17.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 - LBD5_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS12_B73.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 - MADS12_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS12_Mo17.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 - MADS12_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS43_B73.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 - MADS43_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS43_Mo17.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 - MADS43_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS68_B73.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 - MADS68_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS68_Mo17.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 - MADS68_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS69_B73.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 - MADS69_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS69_Mo17.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 - MADS69_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS72_B73.end.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 - MADS72_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS72_Mo17.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 - MADS72_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS73_B73.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 - MADS73_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS73_Mo17.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 - MADS73_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB131_B73.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 - MYB131_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB131_Mo17.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 - MYB131_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB138_B73.end.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 - MYB138_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB138_Mo17.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 - MYB138_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB40_B73.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 - MYB40_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB40_Mo17.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 - MYB40_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB50_B73.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 - MYB50_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB50_Mo17.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 - MYB50_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB73_DED1_Mo17.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 - MYB73_DED1_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB83_B73.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 - MYB83_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB83_Mo17.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 - MYB83_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB94_Mo17.end.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 - MYB94_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYBR101_B73.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 - MYBR101_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYBR101_Mo17.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 - MYBR101_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYBR111_B73.end.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 - MYBR111_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYBR111_Mo17.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 - MYBR111_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYBR17_B73.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 - MYBR17_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYBR17_Mo17.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 - MYBR17_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYBR52_B73.end.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 - MYBR52_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYBR52_Mo17.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 - MYBR52_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYBR58_B73.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 - MYBR58_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYBR58_Mo17.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 - MYBR58_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC115_B73.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 - NAC115_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC115_Mo17.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 - NAC115_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC116_B73.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 - NAC116_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC116_Mo17.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 - NAC116_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC12_B73.end.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 - NAC12_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC12_Mo17.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 - NAC12_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC20_B73.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 - NAC20_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC20_Mo17.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 - NAC20_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC25_B73.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 - NAC25_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC25_Mo17.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 - NAC25_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC27_B73.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 - NAC27_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC27_Mo17.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 - NAC27_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC28_B73.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 - NAC28_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC28_Mo17.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 - NAC28_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC33_B73.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 - NAC33_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC33_Mo17.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 - NAC33_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC3_B73.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 - NAC3_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC3_Mo17.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 - NAC3_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC42_B73.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 - NAC42_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC42_Mo17.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 - NAC42_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC49_B73.end.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 - NAC49_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC49_Mo17.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 - NAC49_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC71_B73.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 - NAC71_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC71_Mo17.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 - NAC71_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC74_B73.end.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 - NAC74_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC74_Mo17.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 - NAC74_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC86_B73.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 - NAC86_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC86_Mo17.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 - NAC86_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC91_Mo17.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 - NAC91_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NFYA1_LEC1_CA5P16_B73.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 - NFYA1_LEC1_CA5P16_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NFYA1_LEC1_CA5P16_Mo17.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 - NFYA1_LEC1_CA5P16_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NKD1_B73.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_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NKD1_Mo17.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_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NKD2_B73.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_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NKD2_Mo17.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_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NLP14_B73.end.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 - NLP14_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NLP14_Mo17.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 - NLP14_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP15_B73.end.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 - SBP15_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP15_Mo17.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 - SBP15_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP1_B73.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 - SBP1_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP1_Mo17.end.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 - SBP1_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP2_B73.end.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 - SBP2_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP2_Mo17.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 - SBP2_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP30_Mo17.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 - SBP30_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP30_rep1_B73.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 - SBP30_rep1_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP30_rep2_B73.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 - SBP30_rep2_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP32_B73.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 - SBP32_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP32_Mo17.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 - SBP32_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP6_Mo17.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 - SBP6_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP8_Mo17.end.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 - SBP8_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP11_B73.end.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 - TCP11_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP11_Mo17.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 - TCP11_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP15_B73.end.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 - TCP15_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP15_Mo17.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 - TCP15_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP2_B73.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 - TCP2_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP2_Mo17.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 - TCP2_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP30_B73.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 - TCP30_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP30_Mo17.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 - TCP30_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP3_Mo17.end.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 - TCP3_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP4_B73.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 - TCP4_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP4_Mo17.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 - TCP4_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP5_B73.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 - TCP5_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP5_Mo17.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 - TCP5_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP8_B73.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 - TCP8_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP8_Mo17.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 - TCP8_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py THX16_B73.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 - THX16_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py THX16_Mo17.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 - THX16_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py THX20_B73.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 - THX20_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py THX20_Mo17.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 - THX20_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py THX26_B73.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 - THX26_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py THX26_Mo17.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 - THX26_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY11_B73.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 - WRKY11_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY11_Mo17.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 - WRKY11_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY125_B73.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 - WRKY125_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY125_Mo17.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 - WRKY125_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY53_B73.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 - WRKY53_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY53_Mo17.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 - WRKY53_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY57_B73.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 - WRKY57_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY57_Mo17.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 - WRKY57_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY64_B73.end.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 - WRKY64_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY64_Mo17.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 - WRKY64_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY82_B73.end.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 - WRKY82_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY82_Mo17.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 - WRKY82_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YAB2_B73.end.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 - YAB2_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YAB2_Mo17.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 - YAB2_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZHD15_B73.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 - ZHD15_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZHD15_Mo17.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 - ZHD15_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZHD1_B73.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 - ZHD1_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZHD1_Mo17.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 - ZHD1_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZHD21_B73.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 - ZHD21_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZHD21_Mo17.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 - ZHD21_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZHD4_B73.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 - ZHD4_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZHD4_Mo17.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 - ZHD4_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZHD5_B73.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 - ZHD5_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZHD5_Mo17.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 - ZHD5_Mo17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZIM2_B73.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 - ZIM2_B73.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZIM2_Mo17.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 - ZIM2_Mo17.1x36mers.unique