python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF14_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF25_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARF35_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ARR5_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH106_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH106_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH149_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BHLH149_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP27_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP2_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP54_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZIP57_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BZR1_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB126_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB2_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB49_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py EREB53_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GATA20_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GATA20_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK20_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK21_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GLK48_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-GST_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB102_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB117_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB122_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB15_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB22_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB54_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB67_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB67_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB68_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF10_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF10_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF24_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF7_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MADS72_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB138_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB94_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYBR111_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYBR52_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC12_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC49_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC74_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NLP14_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP15_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP1_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP2_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP8_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP11_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP15_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TCP3_Mo17.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY64_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY82_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YAB2_B73.end.fastq.gz 75 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/bowtie-indexes/GCA_000005005.6_B73_RefGen_v4_genomic -p 20 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_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.SE.a