/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/2016-11-16-refFlat.fa M3KO1_fast5_pass.fastq > M3KO1_fast5_pass.sam 2>&1 | tee M3KO1_fast5_pass.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/2016-11-16-refFlat.fa M3KO2_fast5_pass.fastq > M3KO2_fast5_pass.sam 2>&1 | tee M3KO2_fast5_pass.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/2016-11-16-refFlat.fa M3P1_fast5_pass.fastq > M3P1_fast5_pass.sam 2>&1 | tee M3P1_fast5_pass.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/2016-11-16-refFlat.fa M3P2_fast5_pass.fastq > M3P2_fast5_pass.sam 2>&1 | tee M3P2_fast5_pass.minimap.logfile.txt