/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 SGNex_A549_directRNA_replicate1_run1.fastq > SGNex_A549_directRNA_replicate1_run1.sam 2>&1 | tee SGNex_A549_directRNA_replicate1_run1.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 SGNex_A549_directRNA_replicate6_run1.fastq > SGNex_A549_directRNA_replicate6_run1.sam 2>&1 | tee SGNex_A549_directRNA_replicate6_run1.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 SGNex_H9_directRNA_replicate1_run1.fastq > SGNex_H9_directRNA_replicate1_run1.sam 2>&1 | tee SGNex_H9_directRNA_replicate1_run1.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 SGNex_Hct116_directRNA_replicate1_run2.fastq > SGNex_Hct116_directRNA_replicate1_run2.sam 2>&1 | tee SGNex_Hct116_directRNA_replicate1_run2.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 SGNex_A549_directRNA_replicate4_run1.fastq > SGNex_A549_directRNA_replicate4_run1.sam 2>&1 | tee SGNex_A549_directRNA_replicate4_run1.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 SGNex_Hct116_directRNA_replicate1_run1.fastq > SGNex_Hct116_directRNA_replicate1_run1.sam 2>&1 | tee SGNex_Hct116_directRNA_replicate1_run1.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 SGNex_Hct116_directRNA_replicate1_run3.fastq > SGNex_Hct116_directRNA_replicate1_run3.sam 2>&1 | tee SGNex_Hct116_directRNA_replicate1_run3.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 SGNex_Hct116_directRNA_replicate2_run1.fastq > SGNex_Hct116_directRNA_replicate2_run1.sam 2>&1 | tee SGNex_Hct116_directRNA_replicate2_run1.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 SGNex_Hct116_directRNA_replicate2_run2.fastq > SGNex_Hct116_directRNA_replicate2_run2.sam 2>&1 | tee SGNex_Hct116_directRNA_replicate2_run2.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 SGNex_Hct116_directRNA_replicate3_run1.fastq > SGNex_Hct116_directRNA_replicate3_run1.sam 2>&1 | tee SGNex_Hct116_directRNA_replicate3_run1.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 SGNex_Hct116_directRNA_replicate3_run4.fastq > SGNex_Hct116_directRNA_replicate3_run4.sam 2>&1 | tee SGNex_Hct116_directRNA_replicate3_run4.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 SGNex_Hek293T_directRNA_replicate4_run1.fastq > SGNex_Hek293T_directRNA_replicate4_run1.sam 2>&1 | tee SGNex_Hek293T_directRNA_replicate4_run1.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 SGNex_Hct116_directRNA_replicate4_run3.fastq > SGNex_Hct116_directRNA_replicate4_run3.sam 2>&1 | tee SGNex_Hct116_directRNA_replicate4_run3.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 SGNex_Hek293T_directRNA_replicate3_run1.fastq > SGNex_Hek293T_directRNA_replicate3_run1.sam 2>&1 | tee SGNex_Hek293T_directRNA_replicate3_run1.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 SGNex_HepG2_directRNA_replicate1_run3.fastq > SGNex_HepG2_directRNA_replicate1_run3.sam 2>&1 | tee SGNex_HepG2_directRNA_replicate1_run3.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 SGNex_HepG2_directRNA_replicate6_run1.fastq > SGNex_HepG2_directRNA_replicate6_run1.sam 2>&1 | tee SGNex_HepG2_directRNA_replicate6_run1.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 SGNex_IM95_directRNA_replicate1_run1.fastq > SGNex_IM95_directRNA_replicate1_run1.sam 2>&1 | tee SGNex_IM95_directRNA_replicate1_run1.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 SGNex_K562_directRNA_replicate4_run1.fastq > SGNex_K562_directRNA_replicate4_run1.sam 2>&1 | tee SGNex_K562_directRNA_replicate4_run1.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 SGNex_K562_directRNA_replicate6_run1.fastq > SGNex_K562_directRNA_replicate6_run1.sam 2>&1 | tee SGNex_K562_directRNA_replicate6_run1.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 SGNex_MCF7_directRNA_replicate3_run1.fastq > SGNex_MCF7_directRNA_replicate3_run1.sam 2>&1 | tee SGNex_MCF7_directRNA_replicate3_run1.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 SGNex_K562_directRNA_replicate5_run1.fastq > SGNex_K562_directRNA_replicate5_run1.sam 2>&1 | tee SGNex_K562_directRNA_replicate5_run1.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 SGNex_MCF7_directRNA_replicate4_run1.fastq > SGNex_MCF7_directRNA_replicate4_run1.sam 2>&1 | tee SGNex_MCF7_directRNA_replicate4_run1.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 SGNex_MCF7-EV_directRNA_replicate1_run1.fastq > SGNex_MCF7-EV_directRNA_replicate1_run1.sam 2>&1 | tee SGNex_MCF7-EV_directRNA_replicate1_run1.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 SGNex_MCF7-EV_directRNA_replicate2_run1.fastq > SGNex_MCF7-EV_directRNA_replicate2_run1.sam 2>&1 | tee SGNex_MCF7-EV_directRNA_replicate2_run1.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 SGNex_Myeloma-N082_directRNA_replicate1_run1.fastq > SGNex_Myeloma-N082_directRNA_replicate1_run1.sam 2>&1 | tee SGNex_Myeloma-N082_directRNA_replicate1_run1.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 SGNex_Myeloma-N104_directRNA_replicate1_run1.fastq > SGNex_Myeloma-N104_directRNA_replicate1_run1.sam 2>&1 | tee SGNex_Myeloma-N104_directRNA_replicate1_run1.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 SGNex_Myeloma-N122_directRNA_replicate1_run1.fastq > SGNex_Myeloma-N122_directRNA_replicate1_run1.sam 2>&1 | tee SGNex_Myeloma-N122_directRNA_replicate1_run1.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 SGNex_NCC24_directRNA_replicate1_run1.fastq > SGNex_NCC24_directRNA_replicate1_run1.sam 2>&1 | tee SGNex_NCC24_directRNA_replicate1_run1.minimap.logfile.txt