/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66.transcriptome.fa L1_rep1.fastq > L1_rep1.sam 2>&1 | tee L1_rep1.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66.transcriptome.fa L1_rep2.fastq > L1_rep2.sam 2>&1 | tee L1_rep2.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66.transcriptome.fa L2_rep1.fastq > L2_rep1.sam 2>&1 | tee L2_rep1.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66.transcriptome.fa L2_rep2.fastq > L2_rep2.sam 2>&1 | tee L2_rep2.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66.transcriptome.fa L3_rep1.fastq > L3_rep1.sam 2>&1 | tee L3_rep1.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66.transcriptome.fa L3_rep2.fastq > L3_rep2.sam 2>&1 | tee L3_rep2.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66.transcriptome.fa L4_rep1.fastq > L4_rep1.sam 2>&1 | tee L4_rep1.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66.transcriptome.fa young_adult_rep1.fastq > young_adult_rep1.sam 2>&1 | tee young_adult_rep1.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66.transcriptome.fa young_adult_rep2.fastq > young_adult_rep2.sam 2>&1 | tee young_adult_rep2.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66.transcriptome.fa adult_rep1.fastq > adult_rep1.sam 2>&1 | tee adult_rep1.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66.transcriptome.fa adult_rep2.fastq > adult_rep2.sam 2>&1 | tee adult_rep2.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2  -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66.transcriptome.fa male_rep1.fastq > male_rep1.sam 2>&1 | tee male_rep1.minimap.logfile.txt