/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 13022019_FAK41746_H9mRNA_unmod_BR2.0.fastq > 13022019_FAK41746_H9mRNA_unmod_BR2.0.sam 2>&1 | tee 13022019_FAK41746_H9mRNA_unmod_BR2.0.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 13022019_FAK41746_H9mRNA_unmod_BR2.1.fastq > 13022019_FAK41746_H9mRNA_unmod_BR2.1.sam 2>&1 | tee 13022019_FAK41746_H9mRNA_unmod_BR2.1.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 13022019_FAK41746_H9mRNA_unmod_BR2.2.fastq > 13022019_FAK41746_H9mRNA_unmod_BR2.2.sam 2>&1 | tee 13022019_FAK41746_H9mRNA_unmod_BR2.2.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 20180122_0753_01222018_FAH15784_H9mRNAcontrol.fastq > 20180122_0753_01222018_FAH15784_H9mRNAcontrol.sam 2>&1 | tee 20180122_0753_01222018_FAH15784_H9mRNAcontrol.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 20180714_0635_14072018_FAH64107_H9mRNA_unmod.fastq > 20180714_0635_14072018_FAH64107_H9mRNA_unmod.sam 2>&1 | tee 20180714_0635_14072018_FAH64107_H9mRNA_unmod.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 20180714_0639_14072018_FAJ05033_H9mRNA_unmod.fastq > 20180714_0639_14072018_FAJ05033_H9mRNA_unmod.sam 2>&1 | tee 20180714_0639_14072018_FAJ05033_H9mRNA_unmod.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 20180801_1153_01082018_FAJ05273_H9mRNA_unmod_biolineprep.fastq > 20180801_1153_01082018_FAJ05273_H9mRNA_unmod_biolineprep.sam 2>&1 | tee 20180801_1153_01082018_FAJ05273_H9mRNA_unmod_biolineprep.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 20180827_1050_27082018_FAK14901_H9mRNA.fastq > 20180827_1050_27082018_FAK14901_H9mRNA.sam 2>&1 | tee 20180827_1050_27082018_FAK14901_H9mRNA.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 20180827_1129_27082018_FAH93704_H9mRNA_RevDFlowCell.0.fastq > 20180827_1129_27082018_FAH93704_H9mRNA_RevDFlowCell.0.sam 2>&1 | tee 20180827_1129_27082018_FAH93704_H9mRNA_RevDFlowCell.0.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 20180827_1129_27082018_FAH93704_H9mRNA_RevDFlowCell.1.fastq > 20180827_1129_27082018_FAH93704_H9mRNA_RevDFlowCell.1.sam 2>&1 | tee 20180827_1129_27082018_FAH93704_H9mRNA_RevDFlowCell.1.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 20180827_1129_27082018_FAH93704_H9mRNA_RevDFlowCell.2.fastq > 20180827_1129_27082018_FAH93704_H9mRNA_RevDFlowCell.2.sam 2>&1 | tee 20180827_1129_27082018_FAH93704_H9mRNA_RevDFlowCell.2.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 20180830_1051_30082018_FAK14702_H9mRNA.fastq > 20180830_1051_30082018_FAK14702_H9mRNA.sam 2>&1 | tee 20180830_1051_30082018_FAK14702_H9mRNA.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 20180919_H9_L41_noRT.fastq > 20180919_H9_L41_noRT.sam 2>&1 | tee 20180919_H9_L41_noRT.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 20190208_0727_08022019_FAK45693_H9mRNA_unmod_BR2.fastq > 20190208_0727_08022019_FAK45693_H9mRNA_unmod_BR2.sam 2>&1 | tee 20190208_0727_08022019_FAK45693_H9mRNA_unmod_BR2.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 20190211_0802_11022019_FAK46537_H9mRNA_unmod_BR2.fastq > 20190211_0802_11022019_FAK46537_H9mRNA_unmod_BR2.sam 2>&1 | tee 20190211_0802_11022019_FAK46537_H9mRNA_unmod_BR2.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 20190211_0804_11092019_FAK48878_H9mRNA_unmod_BR2.fastq > 20190211_0804_11092019_FAK48878_H9mRNA_unmod_BR2.sam 2>&1 | tee 20190211_0804_11092019_FAK48878_H9mRNA_unmod_BR2.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 20190213_0509_13022019_FAK41492_H9mRNA_unmod_BR2.fastq > 20190213_0509_13022019_FAK41492_H9mRNA_unmod_BR2.sam 2>&1 | tee 20190213_0509_13022019_FAK41492_H9mRNA_unmod_BR2.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 20190213_0517_13022019_FAK43432_H9mRNA_unmod_BR2.fastq > 20190213_0517_13022019_FAK43432_H9mRNA_unmod_BR2.sam 2>&1 | tee 20190213_0517_13022019_FAK43432_H9mRNA_unmod_BR2.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 20190213_0946_13022019_FAK43432_H9mRNA_unmod_BR2.fastq > 20190213_0946_13022019_FAK43432_H9mRNA_unmod_BR2.sam 2>&1 | tee 20190213_0946_13022019_FAK43432_H9mRNA_unmod_BR2.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 20190215_1130_15022019_FAK41949_H9mRNA_unmod_BR2.fastq > 20190215_1130_15022019_FAK41949_H9mRNA_unmod_BR2.sam 2>&1 | tee 20190215_1130_15022019_FAK41949_H9mRNA_unmod_BR2.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 20190215_1214_15022019_FAK41933_H9mRNA_unmod_BR2.fastq > 20190215_1214_15022019_FAK41933_H9mRNA_unmod_BR2.sam 2>&1 | tee 20190215_1214_15022019_FAK41933_H9mRNA_unmod_BR2.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 20190715_H9_L41_polyA_noRT.fastq > 20190715_H9_L41_polyA_noRT.sam 2>&1 | tee 20190715_H9_L41_polyA_noRT.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 20200214_H9_L41_withRT.fastq > 20200214_H9_L41_withRT.sam 2>&1 | tee 20200214_H9_L41_withRT.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 20200820_H9_L41_withRT.fastq > 20200820_H9_L41_withRT.sam 2>&1 | tee 20200820_H9_L41_withRT.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 20200824_H9_L41_withRT.fastq > 20200824_H9_L41_withRT.sam 2>&1 | tee 20200824_H9_L41_withRT.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 20200901_H9_L41_withRT.fastq > 20200901_H9_L41_withRT.sam 2>&1 | tee 20200901_H9_L41_withRT.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 20200820_H9_L41_withRT.fastq > 20200820_H9_L41_withRT.sam 2>&1 | tee 20200820_H9_L41_withRT.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 20200824_H9_L41_withRT.fastq > 20200824_H9_L41_withRT.sam 2>&1 | tee 20200824_H9_L41_withRT.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 20200901_H9_L41_withRT.fastq > 20200901_H9_L41_withRT.sam 2>&1 | tee 20200901_H9_L41_withRT.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 20210203_HCT116_7_withRT.fastq > 20210203_HCT116_7_withRT.sam 2>&1 | tee 20210203_HCT116_7_withRT.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 20210203_HCT116_8_withRT.fastq > 20210203_HCT116_8_withRT.sam 2>&1 | tee 20210203_HCT116_8_withRT.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 20210205_HCT116_8_1_withRT.fastq > 20210205_HCT116_8_1_withRT.sam 2>&1 | tee 20210205_HCT116_8_1_withRT.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 20210205_HCT116_8_2_withRT.fastq > 20210205_HCT116_8_2_withRT.sam 2>&1 | tee 20210205_HCT116_8_2_withRT.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 20210324_HCT116_7_withRT.fastq > 20210324_HCT116_7_withRT.sam 2>&1 | tee 20210324_HCT116_7_withRT.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 20210324_HCT116_8_withRT.fastq > 20210324_HCT116_8_withRT.sam 2>&1 | tee 20210324_HCT116_8_withRT.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 20210325_HCT116_7_withRT.fastq > 20210325_HCT116_7_withRT.sam 2>&1 | tee 20210325_HCT116_7_withRT.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 20210325_HCT116_8_withRT.fastq > 20210325_HCT116_8_withRT.sam 2>&1 | tee 20210325_HCT116_8_withRT.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 20210326_HCT116_8_1_withRT.fastq > 20210326_HCT116_8_1_withRT.sam 2>&1 | tee 20210326_HCT116_8_1_withRT.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 20210326_HCT116_8_2_withRT.fastq > 20210326_HCT116_8_2_withRT.sam 2>&1 | tee 20210326_HCT116_8_2_withRT.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 20210629_hct116_8_withRT.fastq > 20210629_hct116_8_withRT.sam 2>&1 | tee 20210629_hct116_8_withRT.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 20210707_hct116_8_withRT.fastq > 20210707_hct116_8_withRT.sam 2>&1 | tee 20210707_hct116_8_withRT.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 20210712_hct116_8_withRT_2.fastq > 20210712_hct116_8_withRT_2.sam 2>&1 | tee 20210712_hct116_8_withRT_2.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 20210712_hct116_8_withRT.fastq > 20210712_hct116_8_withRT.sam 2>&1 | tee 20210712_hct116_8_withRT.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 20210721_hct116_8_withRT.fastq > 20210721_hct116_8_withRT.sam 2>&1 | tee 20210721_hct116_8_withRT.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 20210805_hct116_8_withRT.fastq > 20210805_hct116_8_withRT.sam 2>&1 | tee 20210805_hct116_8_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20210108_mouse_brain_682_4_withRT.fastq > 20210108_mouse_brain_682_4_withRT.sam 2>&1 | tee 20210108_mouse_brain_682_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200725_mouse_brain_675_4_withRT.fastq > 20200725_mouse_brain_675_4_withRT.sam 2>&1 | tee 20200725_mouse_brain_675_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200729_mouse_brain_685_4_withRT.fastq > 20200729_mouse_brain_685_4_withRT.sam 2>&1 | tee 20200729_mouse_brain_685_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200729_mouse_brain_686_4_withRT.fastq > 20200729_mouse_brain_686_4_withRT.sam 2>&1 | tee 20200729_mouse_brain_686_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200802_mouse_brain_682_4_withRT.fastq > 20200802_mouse_brain_682_4_withRT.sam 2>&1 | tee 20200802_mouse_brain_682_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200804_mouse_brain_677_4_withRT.fastq > 20200804_mouse_brain_677_4_withRT.sam 2>&1 | tee 20200804_mouse_brain_677_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200804_mouse_brain_682_4_withRT.fastq > 20200804_mouse_brain_682_4_withRT.sam 2>&1 | tee 20200804_mouse_brain_682_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200806_mouse_brain_676_4_withRT.fastq > 20200806_mouse_brain_676_4_withRT.sam 2>&1 | tee 20200806_mouse_brain_676_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200905_mouse_brain_675_4_withRT.fastq > 20200905_mouse_brain_675_4_withRT.sam 2>&1 | tee 20200905_mouse_brain_675_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200905_mouse_brain_676_4_withRT.fastq > 20200905_mouse_brain_676_4_withRT.sam 2>&1 | tee 20200905_mouse_brain_676_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200907_mouse_brain_685_4_withRT.fastq > 20200907_mouse_brain_685_4_withRT.sam 2>&1 | tee 20200907_mouse_brain_685_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200907_mouse_brain_686_4_withRT.fastq > 20200907_mouse_brain_686_4_withRT.sam 2>&1 | tee 20200907_mouse_brain_686_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200908_mouse_brain_675_4_withRT.fastq > 20200908_mouse_brain_675_4_withRT.sam 2>&1 | tee 20200908_mouse_brain_675_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200908_mouse_brain_677_4_withRT.fastq > 20200908_mouse_brain_677_4_withRT.sam 2>&1 | tee 20200908_mouse_brain_677_4_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.fa 20200719_xenopus_rep1_stage1_withRT.fastq > 20200719_xenopus_rep1_stage1_withRT.sam 2>&1 | tee 20200719_xenopus_rep1_stage1_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20200719_xenopus_rep2_stage1_withRT.fastq > 20200719_xenopus_rep2_stage1_withRT.sam 2>&1 | tee 20200719_xenopus_rep2_stage1_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20200721_xenopus_rep1_stage9_withRT.fastq > 20200721_xenopus_rep1_stage9_withRT.sam 2>&1 | tee 20200721_xenopus_rep1_stage9_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20200721_xenopus_rep2_stage9_withRT.fastq > 20200721_xenopus_rep2_stage9_withRT.sam 2>&1 | tee 20200721_xenopus_rep2_stage9_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20200812_xenopus_rep3_stage1_withRT.fastq > 20200812_xenopus_rep3_stage1_withRT.sam 2>&1 | tee 20200812_xenopus_rep3_stage1_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20200812_xenopus_rep3_stage9_withRT.fastq > 20200812_xenopus_rep3_stage9_withRT.sam 2>&1 | tee 20200812_xenopus_rep3_stage9_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20200814_xenopus_rep2_stage28_withRT.fastq > 20200814_xenopus_rep2_stage28_withRT.sam 2>&1 | tee 20200814_xenopus_rep2_stage28_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20200909_xenopus_rep1_stage1_withRT.fastq > 20200909_xenopus_rep1_stage1_withRT.sam 2>&1 | tee 20200909_xenopus_rep1_stage1_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20201005_xenopus_rep1_stage1_withRT.fastq > 20201005_xenopus_rep1_stage1_withRT.sam 2>&1 | tee 20201005_xenopus_rep1_stage1_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20201005_xenopus_rep1_stage9_withRT.fastq > 20201005_xenopus_rep1_stage9_withRT.sam 2>&1 | tee 20201005_xenopus_rep1_stage9_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20201005_xenopus_rep2_stage1_withRT.fastq > 20201005_xenopus_rep2_stage1_withRT.sam 2>&1 | tee 20201005_xenopus_rep2_stage1_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20201005_xenopus_rep2_stage9_withRT.fastq > 20201005_xenopus_rep2_stage9_withRT.sam 2>&1 | tee 20201005_xenopus_rep2_stage9_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20201005_xenopus_rep3_stage1_withRT.fastq > 20201005_xenopus_rep3_stage1_withRT.sam 2>&1 | tee 20201005_xenopus_rep3_stage1_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20201008_xenopus_rep1_stage28_withRT.fastq > 20201008_xenopus_rep1_stage28_withRT.sam 2>&1 | tee 20201008_xenopus_rep1_stage28_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20201008_xenopus_rep2_stage28_withRT.fastq > 20201008_xenopus_rep2_stage28_withRT.sam 2>&1 | tee 20201008_xenopus_rep2_stage28_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20201008_xenopus_rep3_stage28_withRT.fastq > 20201008_xenopus_rep3_stage28_withRT.sam 2>&1 | tee 20201008_xenopus_rep3_stage28_withRT.minimap.logfile.txt
/oak/stanford/groups/akundaje/marinovg/programs/minimap2-2.17_x64-linux/minimap2 -ax map-ont /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.fa 20201008_xenopus_rep3_stage9_withRT.fastq > 20201008_xenopus_rep3_stage9_withRT.sam 2>&1 | tee 20201008_xenopus_rep3_stage9_withRT.minimap.logfile.txt