python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L16_exp251111_MS756c2_SCD_1hr-arrest_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L17_exp251111_MS756c2_SCD_1hr-arrest_5uM-PhIAA_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L18_exp251111_MS756c2_SCD_1hr-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L19_exp251111_MS756c2_SCD_4hr50min-arres_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L20_exp251111_MS756c2_SCD_4hr50min-arrest_5uM-PhIAA_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260116L21_exp251111_MS756c2_SCD_4hr50min-arrest_10uM-Torin+5uM-PhIAA_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L11_exp260220_MS951_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L12_exp260220_MS951_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L13_exp260220_MS1154_SCD_1hr-arrest_DMSO_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L14_exp260220_MS1154_SCD_4hr45min-arrest_DMSO_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L15_exp260220_MS1154_SCD_1hr-arrest_1uM-1NMPP1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L16_exp260220_MS1154_SCD_4hr45min-arrest_1uM-1NMPP1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L17_exp251017_MS69_SCD_1hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L18_exp251017_MS69_SCD_1hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L19_exp251017_MS69_SCD_2hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L20_exp251017_MS69_SCD_2hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L21_exp251017_MS69_SCD_3hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L22_exp251017_MS69_SCD_3hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L23_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L24_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L25_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L26_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L27_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260226L28_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L01_exp251017_MS69_SCD_4hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L02_exp251017_MS69_SCD_4hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L03_exp251017_MS69_SCD_5hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L04_exp251017_MS69_SCD_5hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L05_exp251017_MS69_SCD_6hr-arrest_OD-0.1_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig -notitle -RPM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes 2026-03-17-MS260227L06_exp251017_MS69_SCD_6hr-arrest_OD-0.3_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25