python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-A-YPD-input/2018-02-13-A-YPD-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-A-YPD-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-B-YPD-Pol2pS2/2018-02-13-B-YPD-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-B-YPD-Pol2pS2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-C-SCE_input/2018-02-13-C-SCE_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-C-SCE_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-D-SCE-Pol2pS2/2018-02-13-D-SCE-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-D-SCE-Pol2pS2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-E-SCE-H3/2018-02-13-E-SCE-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-E-SCE-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-F-SCE-CTD/2018-02-13-F-SCE-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-F-SCE-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-G-YPD-CTD/2018-02-13-G-YPD-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-G-YPD-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-H-SCD_noAA-input/2018-02-13-H-SCD_noAA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-H-SCD_noAA-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-I-SCD_Rpb1_AA-input/2018-02-13-I-SCD_Rpb1_AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-I-SCD_Rpb1_AA-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-J-SCD_TBP-AA-input/2018-02-13-J-SCD_TBP-AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-J-SCD_TBP-AA-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-K-SCD_noAA-H3/2018-02-13-K-SCD_noAA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-K-SCD_noAA-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-L-SCD_Rpb1_AA-H3/2018-02-13-L-SCD_Rpb1_AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-L-SCD_Rpb1_AA-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-M-SCD_TBP-AA-H3/2018-02-13-M-SCD_TBP-AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-M-SCD_TBP-AA-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-N-YPD-Rpb3/2018-02-13-N-YPD-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-N-YPD-Rpb3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-O-SCE-Rpb3/2018-02-13-O-SCE-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-O-SCE-Rpb3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-P-SCD_noAA-CTD/2018-02-13-P-SCD_noAA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-P-SCD_noAA-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-Q-SCD_Rpb1_AA-CTD/2018-02-13-Q-SCD_Rpb1_AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-Q-SCD_Rpb1_AA-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-R-SCD_TBP-AA-CTD/2018-02-13-R-SCD_TBP-AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-R-SCD_TBP-AA-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-S-SCD_noAA-Rpb3/2018-02-13-S-SCD_noAA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-S-SCD_noAA-Rpb3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-T-YPD-Pol2pS5_C/2018-02-13-T-YPD-Pol2pS5_C.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-T-YPD-Pol2pS5_C.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-U-YPD-Pol2pS5_D/2018-02-13-U-YPD-Pol2pS5_D.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-U-YPD-Pol2pS5_D.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-V-YPD-Pol2pS5_E/2018-02-13-V-YPD-Pol2pS5_E.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-V-YPD-Pol2pS5_E.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-W-SCD_Rpb1_AA-Rpb3/2018-02-13-W-SCD_Rpb1_AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-W-SCD_Rpb1_AA-Rpb3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-X-SCD_TBP-AA-Rpb3/2018-02-13-X-SCD_TBP-AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-02-13-X-SCD_TBP-AA-Rpb3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_0.0625/2018-04-20-H3-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-H3-SC_ratio_0.0625.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_0.25/2018-04-20-H3-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-H3-SC_ratio_0.25.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_0.5/2018-04-20-H3-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-H3-SC_ratio_0.5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_1/2018-04-20-H3-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-H3-SC_ratio_1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_16/2018-04-20-H3-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-H3-SC_ratio_16.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_2/2018-04-20-H3-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-H3-SC_ratio_2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_4/2018-04-20-H3-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-H3-SC_ratio_4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_0.0625/2018-04-20-Input-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Input-SC_ratio_0.0625.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_0.25/2018-04-20-Input-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Input-SC_ratio_0.25.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_0.5/2018-04-20-Input-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Input-SC_ratio_0.5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_1/2018-04-20-Input-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Input-SC_ratio_1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_16/2018-04-20-Input-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Input-SC_ratio_16.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_2/2018-04-20-Input-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Input-SC_ratio_2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_4/2018-04-20-Input-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Input-SC_ratio_4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_0.0625/2018-04-20-Pol2pS2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2pS2-SC_ratio_0.0625.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_0.25/2018-04-20-Pol2pS2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2pS2-SC_ratio_0.25.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_0.5/2018-04-20-Pol2pS2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2pS2-SC_ratio_0.5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_1/2018-04-20-Pol2pS2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2pS2-SC_ratio_1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_16/2018-04-20-Pol2pS2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2pS2-SC_ratio_16.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_2/2018-04-20-Pol2pS2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2pS2-SC_ratio_2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_4/2018-04-20-Pol2pS2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2pS2-SC_ratio_4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS5-L1/2018-04-20-Pol2pS5-L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2pS5-L1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS5-L2/2018-04-20-Pol2pS5-L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2pS5-L2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS5-L3/2018-04-20-Pol2pS5-L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2pS5-L3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS5-L4/2018-04-20-Pol2pS5-L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2pS5-L4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_0.0625/2018-04-20-Pol2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2-SC_ratio_0.0625.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_0.25/2018-04-20-Pol2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2-SC_ratio_0.25.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_0.5/2018-04-20-Pol2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2-SC_ratio_0.5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_1/2018-04-20-Pol2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2-SC_ratio_1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_16/2018-04-20-Pol2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2-SC_ratio_16.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_2/2018-04-20-Pol2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2-SC_ratio_2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_4/2018-04-20-Pol2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-04-20-Pol2-SC_ratio_4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-0nM-H3-180529_L13/2018-06-16-MS63-0nM-H3-180529_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-0nM-H3-180529_L13.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-0nM-Input-180529_L1/2018-06-16-MS63-0nM-Input-180529_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-0nM-Input-180529_L1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-0nM-Pol2-180529_L4/2018-06-16-MS63-0nM-Pol2-180529_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-0nM-Pol2-180529_L4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7/2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10/2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-10nM-H3-180529_L14/2018-06-16-MS63-10nM-H3-180529_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-10nM-H3-180529_L14.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-10nM-Input-180529_L2/2018-06-16-MS63-10nM-Input-180529_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-10nM-Input-180529_L2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-10nM-Pol2-180529_L5/2018-06-16-MS63-10nM-Pol2-180529_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-10nM-Pol2-180529_L5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8/2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11/2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-30nM-H3-180529_L15/2018-06-16-MS63-30nM-H3-180529_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-30nM-H3-180529_L15.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-30nM-Input-180529_L3/2018-06-16-MS63-30nM-Input-180529_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-30nM-Input-180529_L3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-30nM-Pol2-180529_L6/2018-06-16-MS63-30nM-Pol2-180529_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-30nM-Pol2-180529_L6.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9/2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12/2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS80-H3-180525_L14/2018-06-16-MS80-H3-180525_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS80-H3-180525_L14.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS80-Input-180525_L2/2018-06-16-MS80-Input-180525_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS80-Input-180525_L2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS80-Pol2-180525_L5/2018-06-16-MS80-Pol2-180525_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS80-Pol2-180525_L5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS80-RNAPII_pS2-180525_L8/2018-06-16-MS80-RNAPII_pS2-180525_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS80-RNAPII_pS2-180525_L8.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS80-RNAPII_pS5-180525_L11/2018-06-16-MS80-RNAPII_pS5-180525_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS80-RNAPII_pS5-180525_L11.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS81-H3-180525_L15/2018-06-16-MS81-H3-180525_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS81-H3-180525_L15.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS81-Input-180525_L3/2018-06-16-MS81-Input-180525_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS81-Input-180525_L3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS81-Pol2-180525_L6/2018-06-16-MS81-Pol2-180525_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS81-Pol2-180525_L6.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS81-RNAPII_pS2-180525_L9/2018-06-16-MS81-RNAPII_pS2-180525_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS81-RNAPII_pS2-180525_L9.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS81-RNAPII_pS5-180525_L12/2018-06-16-MS81-RNAPII_pS5-180525_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-MS81-RNAPII_pS5-180525_L12.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21/2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1/2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11/2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22/2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2/2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12/2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23/2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3/2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13/2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24/2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4/2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14/2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25/2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5/2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15/2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_0min_+rap-H3-180522_L26/2018-06-16-TBP_AA_0min_+rap-H3-180522_L26.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_0min_+rap-H3-180522_L26.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_0min_+rap-Input-180522_L6/2018-06-16-TBP_AA_0min_+rap-Input-180522_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_0min_+rap-Input-180522_L6.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16/2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_10min_+rap-H3-180522_L27/2018-06-16-TBP_AA_10min_+rap-H3-180522_L27.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_10min_+rap-H3-180522_L27.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_10min_+rap-Input-180522_L7/2018-06-16-TBP_AA_10min_+rap-Input-180522_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_10min_+rap-Input-180522_L7.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17/2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_20min_+rap-H3-180522_L28/2018-06-16-TBP_AA_20min_+rap-H3-180522_L28.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_20min_+rap-H3-180522_L28.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_20min_+rap-Input-180522_L8/2018-06-16-TBP_AA_20min_+rap-Input-180522_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_20min_+rap-Input-180522_L8.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18/2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_30min_+rap-H3-180522_L29/2018-06-16-TBP_AA_30min_+rap-H3-180522_L29.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_30min_+rap-H3-180522_L29.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_30min_+rap-Input-180522_L9/2018-06-16-TBP_AA_30min_+rap-Input-180522_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_30min_+rap-Input-180522_L9.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19/2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_60min_+rap-H3-180522_L30/2018-06-16-TBP_AA_60min_+rap-H3-180522_L30.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_60min_+rap-H3-180522_L30.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_60min_+rap-Input-180522_L10/2018-06-16-TBP_AA_60min_+rap-Input-180522_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_60min_+rap-Input-180522_L10.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20/2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-H3-180525_L13/2018-06-16-WT_OD_0.1-H3-180525_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.1-H3-180525_L13.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-H3-180531_L19/2018-06-16-WT_OD_0.1-H3-180531_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.1-H3-180531_L19.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-Input-180525_L1/2018-06-16-WT_OD_0.1-Input-180525_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.1-Input-180525_L1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-Input-180531_L1/2018-06-16-WT_OD_0.1-Input-180531_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.1-Input-180531_L1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-Pol2-180525_L4/2018-06-16-WT_OD_0.1-Pol2-180525_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.1-Pol2-180525_L4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-Pol2-180531_L7/2018-06-16-WT_OD_0.1-Pol2-180531_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.1-Pol2-180531_L7.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7/2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13/2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10/2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.2-H3-180531_L20/2018-06-16-WT_OD_0.2-H3-180531_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.2-H3-180531_L20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.2-Input-180531_L2/2018-06-16-WT_OD_0.2-Input-180531_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.2-Input-180531_L2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.2-Pol2-180531_L8/2018-06-16-WT_OD_0.2-Pol2-180531_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.2-Pol2-180531_L8.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14/2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.3-H3-180531_L21/2018-06-16-WT_OD_0.3-H3-180531_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.3-H3-180531_L21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.3-Input-180531_L3/2018-06-16-WT_OD_0.3-Input-180531_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.3-Input-180531_L3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.3-Pol2-180531_L9/2018-06-16-WT_OD_0.3-Pol2-180531_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.3-Pol2-180531_L9.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15/2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.4-H3-180531_L22/2018-06-16-WT_OD_0.4-H3-180531_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.4-H3-180531_L22.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.4-Input-180531_L4/2018-06-16-WT_OD_0.4-Input-180531_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.4-Input-180531_L4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.4-Pol2-180531_L10/2018-06-16-WT_OD_0.4-Pol2-180531_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.4-Pol2-180531_L10.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16/2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.5-H3-180531_L23/2018-06-16-WT_OD_0.5-H3-180531_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.5-H3-180531_L23.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.5-Input-180531_L5/2018-06-16-WT_OD_0.5-Input-180531_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.5-Input-180531_L5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.5-Pol2-180531_L11/2018-06-16-WT_OD_0.5-Pol2-180531_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.5-Pol2-180531_L11.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17/2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.6-H3-180531_L24/2018-06-16-WT_OD_0.6-H3-180531_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.6-H3-180531_L24.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.6-Input-180531_L6/2018-06-16-WT_OD_0.6-Input-180531_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.6-Input-180531_L6.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.6-Pol2-180531_L12/2018-06-16-WT_OD_0.6-Pol2-180531_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.6-Pol2-180531_L12.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18/2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS80_15-H3-rep1-whi5/2018-07-12-MS80_15-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-07-12-MS80_15-H3-rep1-whi5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS80_15-H3-rep2-whi5/2018-07-12-MS80_15-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-07-12-MS80_15-H3-rep2-whi5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS80_15-input-whi5/2018-07-12-MS80_15-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-07-12-MS80_15-input-whi5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS80_5-H3-rep1-whi5/2018-07-12-MS80_5-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-07-12-MS80_5-H3-rep1-whi5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS80_5-H3-rep2-whi5/2018-07-12-MS80_5-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-07-12-MS80_5-H3-rep2-whi5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS80_5-input-whi5/2018-07-12-MS80_5-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-07-12-MS80_5-input-whi5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS81_15-H3-rep1-cln3/2018-07-12-MS81_15-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-07-12-MS81_15-H3-rep1-cln3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS81_15-H3-rep2-cln3/2018-07-12-MS81_15-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-07-12-MS81_15-H3-rep2-cln3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS81_15-input-cln3/2018-07-12-MS81_15-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-07-12-MS81_15-input-cln3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS81_5-H3-rep1-cln3/2018-07-12-MS81_5-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-07-12-MS81_5-H3-rep1-cln3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS81_5-H3-rep2-cln3/2018-07-12-MS81_5-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-07-12-MS81_5-H3-rep2-cln3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS81_5-input-cln3/2018-07-12-MS81_5-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-07-12-MS81_5-input-cln3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L10-MS80-AB21/2018-09-13-180718-L10-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L10-MS80-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L11-MS81-input/2018-09-13-180718-L11-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L11-MS81-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L12-MS81-input-2/2018-09-13-180718-L12-MS81-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L12-MS81-input-2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L13-MS81-AB5/2018-09-13-180718-L13-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L13-MS81-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L14-MS81-AB20/2018-09-13-180718-L14-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L14-MS81-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L15-MS81-AB21/2018-09-13-180718-L15-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L15-MS81-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L16-MS63-0nM-input/2018-09-13-180718-L16-MS63-0nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L16-MS63-0nM-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L17-MS63-0nM-input-2/2018-09-13-180718-L17-MS63-0nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L17-MS63-0nM-input-2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L18-MS63-0nM-AB5/2018-09-13-180718-L18-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L18-MS63-0nM-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L19-MS63-0nM-AB20/2018-09-13-180718-L19-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L19-MS63-0nM-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L1-MS1-input/2018-09-13-180718-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L1-MS1-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L20-MS63-0nM-AB21/2018-09-13-180718-L20-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L20-MS63-0nM-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L21-MS63-10nM-input/2018-09-13-180718-L21-MS63-10nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L21-MS63-10nM-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L22-MS63-10nM-input-2/2018-09-13-180718-L22-MS63-10nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L22-MS63-10nM-input-2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L23-MS63-10nM-AB5/2018-09-13-180718-L23-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L23-MS63-10nM-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L24-MS63-10nM-AB20/2018-09-13-180718-L24-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L24-MS63-10nM-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L25-MS63-10nM-AB21/2018-09-13-180718-L25-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L25-MS63-10nM-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L26-MS63-30nM-input/2018-09-13-180718-L26-MS63-30nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L26-MS63-30nM-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L27-MS63-30nM-input-2/2018-09-13-180718-L27-MS63-30nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L27-MS63-30nM-input-2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L28-MS63-30nM-AB5/2018-09-13-180718-L28-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L28-MS63-30nM-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L29-MS63-30nM-AB20/2018-09-13-180718-L29-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L29-MS63-30nM-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L2-MS1-input-2/2018-09-13-180718-L2-MS1-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L2-MS1-input-2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L30-MS63-30nM-AB21/2018-09-13-180718-L30-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L30-MS63-30nM-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L3-MS1-AB5/2018-09-13-180718-L3-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L3-MS1-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L4-MS1-AB20/2018-09-13-180718-L4-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L4-MS1-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L5-MS1-AB21/2018-09-13-180718-L5-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L5-MS1-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L6-MS80-input/2018-09-13-180718-L6-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L6-MS80-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L7-MS80-input-2/2018-09-13-180718-L7-MS80-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L7-MS80-input-2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L8-MS80-AB5/2018-09-13-180718-L8-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L8-MS80-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L9-MS80-AB20/2018-09-13-180718-L9-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180718-L9-MS80-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L10-MS63-10nM-AB5/2018-09-13-180723-L10-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L10-MS63-10nM-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L11-MS63-10nM-AB20/2018-09-13-180723-L11-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L11-MS63-10nM-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L12-MS63-10nM-AB21/2018-09-13-180723-L12-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L12-MS63-10nM-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L13-MS63-30nM-input2/2018-09-13-180723-L13-MS63-30nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L13-MS63-30nM-input2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L14-MS63-30nM-AB1/2018-09-13-180723-L14-MS63-30nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L14-MS63-30nM-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L15-MS63-30nM-AB4/2018-09-13-180723-L15-MS63-30nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L15-MS63-30nM-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L16-MS63-30nM-AB5/2018-09-13-180723-L16-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L16-MS63-30nM-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L17-MS63-30nM-AB20/2018-09-13-180723-L17-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L17-MS63-30nM-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L18-MS63-30nM-AB21/2018-09-13-180723-L18-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L18-MS63-30nM-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L1-MS63-0nM-input1/2018-09-13-180723-L1-MS63-0nM-input1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L1-MS63-0nM-input1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L2-MS63-0nM-AB1/2018-09-13-180723-L2-MS63-0nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L2-MS63-0nM-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L3-MS63-0nM-AB4/2018-09-13-180723-L3-MS63-0nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L3-MS63-0nM-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L4-MS63-0nM-AB5/2018-09-13-180723-L4-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L4-MS63-0nM-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L5-MS63-0nM-AB20/2018-09-13-180723-L5-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L5-MS63-0nM-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L6-MS63-0nM-AB21/2018-09-13-180723-L6-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L6-MS63-0nM-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L7-MS63-10nM-input2/2018-09-13-180723-L7-MS63-10nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L7-MS63-10nM-input2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L8-MS63-10nM-AB1/2018-09-13-180723-L8-MS63-10nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L8-MS63-10nM-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L9-MS63-10nM-AB4/2018-09-13-180723-L9-MS63-10nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180723-L9-MS63-10nM-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L10-MS80-AB5/2018-09-13-180731-L10-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L10-MS80-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L11-MS80-AB20/2018-09-13-180731-L11-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L11-MS80-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L12-MS80-AB21/2018-09-13-180731-L12-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L12-MS80-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L13-MS81-input/2018-09-13-180731-L13-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L13-MS81-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L14-MS81-AB1/2018-09-13-180731-L14-MS81-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L14-MS81-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L15-MS81-AB4/2018-09-13-180731-L15-MS81-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L15-MS81-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L16-MS81-AB5/2018-09-13-180731-L16-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L16-MS81-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L17-MS81-AB20/2018-09-13-180731-L17-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L17-MS81-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L18-MS81-AB21/2018-09-13-180731-L18-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L18-MS81-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L19-MS55-1-input/2018-09-13-180731-L19-MS55-1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L19-MS55-1-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L1-MS1-input/2018-09-13-180731-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L1-MS1-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L20-MS55-1-AB1/2018-09-13-180731-L20-MS55-1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L20-MS55-1-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L21-MS55-1-AB4/2018-09-13-180731-L21-MS55-1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L21-MS55-1-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L22-MS55-1-AB5/2018-09-13-180731-L22-MS55-1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L22-MS55-1-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L23-MS55-1-AB20/2018-09-13-180731-L23-MS55-1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L23-MS55-1-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L24-MS55-1-AB21/2018-09-13-180731-L24-MS55-1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L24-MS55-1-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L25-MS55-2-input/2018-09-13-180731-L25-MS55-2-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L25-MS55-2-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L26-MS55-2-AB1/2018-09-13-180731-L26-MS55-2-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L26-MS55-2-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L27-MS55-2-AB4/2018-09-13-180731-L27-MS55-2-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L27-MS55-2-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L28-MS55-2-AB5/2018-09-13-180731-L28-MS55-2-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L28-MS55-2-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L29-MS55-2-AB20/2018-09-13-180731-L29-MS55-2-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L29-MS55-2-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L2-MS1-AB1/2018-09-13-180731-L2-MS1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L2-MS1-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L30-MS55-2-AB21/2018-09-13-180731-L30-MS55-2-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L30-MS55-2-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L31-MS55-3-input/2018-09-13-180731-L31-MS55-3-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L31-MS55-3-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L32-MS55-3-AB1/2018-09-13-180731-L32-MS55-3-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L32-MS55-3-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L33-MS55-3-AB4/2018-09-13-180731-L33-MS55-3-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L33-MS55-3-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L34-MS55-3-AB5/2018-09-13-180731-L34-MS55-3-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L34-MS55-3-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L35-MS55-3-AB20/2018-09-13-180731-L35-MS55-3-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L35-MS55-3-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L36-MS55-3-AB21/2018-09-13-180731-L36-MS55-3-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L36-MS55-3-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L37-MS55-4-input/2018-09-13-180731-L37-MS55-4-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L37-MS55-4-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L38-MS55-4-AB1/2018-09-13-180731-L38-MS55-4-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L38-MS55-4-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L39-MS55-4-AB4/2018-09-13-180731-L39-MS55-4-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L39-MS55-4-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L3-MS1-AB4/2018-09-13-180731-L3-MS1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L3-MS1-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L40-MS55-4-AB5/2018-09-13-180731-L40-MS55-4-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L40-MS55-4-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L41-MS55-4-AB20/2018-09-13-180731-L41-MS55-4-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L41-MS55-4-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L42-MS55-4-AB21/2018-09-13-180731-L42-MS55-4-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L42-MS55-4-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L4-MS1-AB5/2018-09-13-180731-L4-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L4-MS1-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L5-MS1-AB20/2018-09-13-180731-L5-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L5-MS1-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L6-MS1-AB21/2018-09-13-180731-L6-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L6-MS1-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L7-MS80-input/2018-09-13-180731-L7-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L7-MS80-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L8-MS80-AB1/2018-09-13-180731-L8-MS80-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L8-MS80-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L9-MS80-AB4/2018-09-13-180731-L9-MS80-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-09-13-180731-L9-MS80-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20/2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s1-1-180917_L01_MS230_DMSO_input/2018-10-14-s1-1-180917_L01_MS230_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s1-1-180917_L01_MS230_DMSO_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s11-3-180917_L11_MS232_DMSO_input/2018-10-14-s11-3-180917_L11_MS232_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s11-3-180917_L11_MS232_DMSO_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1/2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4/2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5/2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20/2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s16-4-180917_L16_MS230_RAPA_input/2018-10-14-s16-4-180917_L16_MS230_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s16-4-180917_L16_MS230_RAPA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1/2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4/2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5/2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20/2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1/2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s21-5-180917_L21_MS231_RAPA_input/2018-10-14-s21-5-180917_L21_MS231_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s21-5-180917_L21_MS231_RAPA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1/2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4/2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5/2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20/2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s26-6-180917_L26_MS232_RAPA_input/2018-10-14-s26-6-180917_L26_MS232_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s26-6-180917_L26_MS232_RAPA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1/2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4/2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5/2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20/2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4/2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s76-23-180821_L01_MS1_input/2018-10-14-s76-23-180821_L01_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s76-23-180821_L01_MS1_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s77-23-180821_L02_MS1_AB20/2018-10-14-s77-23-180821_L02_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s77-23-180821_L02_MS1_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s78-23-180821_L03_MS1_AB39/2018-10-14-s78-23-180821_L03_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s78-23-180821_L03_MS1_AB39.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s79-23-180821_L04_MS1_AB42/2018-10-14-s79-23-180821_L04_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s79-23-180821_L04_MS1_AB42.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s80-23-180821_L05_MS1_AB43/2018-10-14-s80-23-180821_L05_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s80-23-180821_L05_MS1_AB43.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s81-23-180821_L06_MS1_AB44/2018-10-14-s81-23-180821_L06_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s81-23-180821_L06_MS1_AB44.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4/2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s82-23-180821_L07_MS1_AB45/2018-10-14-s82-23-180821_L07_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s82-23-180821_L07_MS1_AB45.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s83-23-180821_L08_MS1_AB46/2018-10-14-s83-23-180821_L08_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s83-23-180821_L08_MS1_AB46.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s84-23-180821_L09_MS1_AB47/2018-10-14-s84-23-180821_L09_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s84-23-180821_L09_MS1_AB47.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s85-23-180821_L10_MS1_AB48/2018-10-14-s85-23-180821_L10_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s85-23-180821_L10_MS1_AB48.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s86-24-180827_L1_MS1_input/2018-10-14-s86-24-180827_L1_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s86-24-180827_L1_MS1_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s87-24-180827_L2_MS1_AB20/2018-10-14-s87-24-180827_L2_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s87-24-180827_L2_MS1_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s88-24-180827_L3_MS1_AB39/2018-10-14-s88-24-180827_L3_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s88-24-180827_L3_MS1_AB39.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s89-24-180827_L4_MS1_AB41/2018-10-14-s89-24-180827_L4_MS1_AB41.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s89-24-180827_L4_MS1_AB41.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s90-24-180827_L5_MS1_AB42/2018-10-14-s90-24-180827_L5_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s90-24-180827_L5_MS1_AB42.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s91-24-180827_L6_MS1_AB43/2018-10-14-s91-24-180827_L6_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s91-24-180827_L6_MS1_AB43.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5/2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s92-24-180827_L7_MS1_AB44/2018-10-14-s92-24-180827_L7_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s92-24-180827_L7_MS1_AB44.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s93-24-180827_L8_MS1_AB45/2018-10-14-s93-24-180827_L8_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s93-24-180827_L8_MS1_AB45.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s94-24-180827_L9_MS1_AB46/2018-10-14-s94-24-180827_L9_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s94-24-180827_L9_MS1_AB46.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s95-24-180827_L10_MS1_AB47/2018-10-14-s95-24-180827_L10_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s95-24-180827_L10_MS1_AB47.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s96-24-180827_L11_MS1_AB48/2018-10-14-s96-24-180827_L11_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2018-10-14-s96-24-180827_L11_MS1_AB48.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L01_MS1_input-S01_A/2019-01-03-181105L01_MS1_input-S01_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L01_MS1_input-S01_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L02_MS80_input-S02_A/2019-01-03-181105L02_MS80_input-S02_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L02_MS80_input-S02_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L03_MS81_input-S03_A/2019-01-03-181105L03_MS81_input-S03_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L03_MS81_input-S03_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L04_MS63_0nM_input-S04_A/2019-01-03-181105L04_MS63_0nM_input-S04_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L04_MS63_0nM_input-S04_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L05_MS63_10nM_input-S05_A/2019-01-03-181105L05_MS63_10nM_input-S05_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L05_MS63_10nM_input-S05_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L06_MS63_30nM_input-S06_A/2019-01-03-181105L06_MS63_30nM_input-S06_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L06_MS63_30nM_input-S06_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L07_MS1_AB20-S07_A/2019-01-03-181105L07_MS1_AB20-S07_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L07_MS1_AB20-S07_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L08_MS80_AB20-S08_A/2019-01-03-181105L08_MS80_AB20-S08_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L08_MS80_AB20-S08_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L09_MS81_AB20-S09_A/2019-01-03-181105L09_MS81_AB20-S09_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L09_MS81_AB20-S09_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L10_MS63_0nM_AB20-S10_A/2019-01-03-181105L10_MS63_0nM_AB20-S10_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L10_MS63_0nM_AB20-S10_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L11_MS63_10nM_AB20-S11_A/2019-01-03-181105L11_MS63_10nM_AB20-S11_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L11_MS63_10nM_AB20-S11_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L12_MS63_30nM_AB20-S12_A/2019-01-03-181105L12_MS63_30nM_AB20-S12_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L12_MS63_30nM_AB20-S12_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L13_MS1_AB21-S13_A/2019-01-03-181105L13_MS1_AB21-S13_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L13_MS1_AB21-S13_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L14_MS80_AB21-S14_A/2019-01-03-181105L14_MS80_AB21-S14_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L14_MS80_AB21-S14_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L15_MS81_AB21-S15_A/2019-01-03-181105L15_MS81_AB21-S15_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L15_MS81_AB21-S15_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L16_MS63_0nM_AB21-S16_A/2019-01-03-181105L16_MS63_0nM_AB21-S16_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L16_MS63_0nM_AB21-S16_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L17_MS63_10nM_AB21-S17_A/2019-01-03-181105L17_MS63_10nM_AB21-S17_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L17_MS63_10nM_AB21-S17_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L18_MS63_30nM_AB21-S18_A/2019-01-03-181105L18_MS63_30nM_AB21-S18_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L18_MS63_30nM_AB21-S18_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L19_MS1_AB39-S19_A/2019-01-03-181105L19_MS1_AB39-S19_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L19_MS1_AB39-S19_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L20_MS80_AB39-S20_A/2019-01-03-181105L20_MS80_AB39-S20_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L20_MS80_AB39-S20_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L21_MS81_AB39-S21_A/2019-01-03-181105L21_MS81_AB39-S21_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L21_MS81_AB39-S21_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L22_MS63_0nM_AB39-S22_A/2019-01-03-181105L22_MS63_0nM_AB39-S22_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L22_MS63_0nM_AB39-S22_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L23_MS63_10nM_AB39-S23_A/2019-01-03-181105L23_MS63_10nM_AB39-S23_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L23_MS63_10nM_AB39-S23_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L24_MS63_30nM_AB39-S24_A/2019-01-03-181105L24_MS63_30nM_AB39-S24_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L24_MS63_30nM_AB39-S24_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L25_MS1_AB41-S25_A/2019-01-03-181105L25_MS1_AB41-S25_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L25_MS1_AB41-S25_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L26_MS80_AB41-S26_A/2019-01-03-181105L26_MS80_AB41-S26_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L26_MS80_AB41-S26_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L27_MS81_AB41-S27_A/2019-01-03-181105L27_MS81_AB41-S27_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L27_MS81_AB41-S27_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L28_MS63_0nM_AB41-S28_A/2019-01-03-181105L28_MS63_0nM_AB41-S28_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L28_MS63_0nM_AB41-S28_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L29_MS63_10nM_AB41-S29_A/2019-01-03-181105L29_MS63_10nM_AB41-S29_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L29_MS63_10nM_AB41-S29_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L30_MS63_30nM_AB41-S30_A/2019-01-03-181105L30_MS63_30nM_AB41-S30_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L30_MS63_30nM_AB41-S30_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L31_MS1_AB42-S31_A/2019-01-03-181105L31_MS1_AB42-S31_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L31_MS1_AB42-S31_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L32_MS80_AB42-S32_A/2019-01-03-181105L32_MS80_AB42-S32_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L32_MS80_AB42-S32_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L33_MS81_AB42-S33_A/2019-01-03-181105L33_MS81_AB42-S33_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L33_MS81_AB42-S33_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L34_MS63_0nM_AB42-S34_A/2019-01-03-181105L34_MS63_0nM_AB42-S34_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L34_MS63_0nM_AB42-S34_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L35_MS63_10nM_AB42-S35_A/2019-01-03-181105L35_MS63_10nM_AB42-S35_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L35_MS63_10nM_AB42-S35_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L36_MS63_30nM_AB42-S36_A/2019-01-03-181105L36_MS63_30nM_AB42-S36_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L36_MS63_30nM_AB42-S36_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L37_MS1_AB43-S37_A/2019-01-03-181105L37_MS1_AB43-S37_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L37_MS1_AB43-S37_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L38_MS80_AB43-S38_A/2019-01-03-181105L38_MS80_AB43-S38_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L38_MS80_AB43-S38_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L39_MS81_AB43-S39_A/2019-01-03-181105L39_MS81_AB43-S39_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L39_MS81_AB43-S39_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L40_MS63_0nM_AB43-S40_A/2019-01-03-181105L40_MS63_0nM_AB43-S40_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L40_MS63_0nM_AB43-S40_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L41_MS63_10nM_AB43-S41_A/2019-01-03-181105L41_MS63_10nM_AB43-S41_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L41_MS63_10nM_AB43-S41_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L42_MS63_30nM_AB43-S42_A/2019-01-03-181105L42_MS63_30nM_AB43-S42_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L42_MS63_30nM_AB43-S42_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L43_MS1_AB44-S43_A/2019-01-03-181105L43_MS1_AB44-S43_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L43_MS1_AB44-S43_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L44_MS80_AB44-S44_A/2019-01-03-181105L44_MS80_AB44-S44_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L44_MS80_AB44-S44_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L45_MS81_AB44-S45_A/2019-01-03-181105L45_MS81_AB44-S45_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L45_MS81_AB44-S45_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L46_MS63_0nM_AB44-S46_A/2019-01-03-181105L46_MS63_0nM_AB44-S46_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L46_MS63_0nM_AB44-S46_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L47_MS63_10nM_AB44-S47_A/2019-01-03-181105L47_MS63_10nM_AB44-S47_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L47_MS63_10nM_AB44-S47_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L48_MS63_30nM_AB44-S48_A/2019-01-03-181105L48_MS63_30nM_AB44-S48_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L48_MS63_30nM_AB44-S48_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L49_MS1_AB45-S49_A/2019-01-03-181105L49_MS1_AB45-S49_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L49_MS1_AB45-S49_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L50_MS80_AB45-S50_A/2019-01-03-181105L50_MS80_AB45-S50_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L50_MS80_AB45-S50_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L51_MS81_AB45-S51_A/2019-01-03-181105L51_MS81_AB45-S51_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L51_MS81_AB45-S51_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L52_MS63_0nM_AB45-S52_A/2019-01-03-181105L52_MS63_0nM_AB45-S52_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L52_MS63_0nM_AB45-S52_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L53_MS63_10nM_AB45-S53_A/2019-01-03-181105L53_MS63_10nM_AB45-S53_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L53_MS63_10nM_AB45-S53_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L54_MS63_30nM_AB45-S54_A/2019-01-03-181105L54_MS63_30nM_AB45-S54_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L54_MS63_30nM_AB45-S54_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L55_MS1_AB46-S55_A/2019-01-03-181105L55_MS1_AB46-S55_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L55_MS1_AB46-S55_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L56_MS80_AB46-S56_A/2019-01-03-181105L56_MS80_AB46-S56_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L56_MS80_AB46-S56_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L57_MS81_AB46-S57_A/2019-01-03-181105L57_MS81_AB46-S57_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L57_MS81_AB46-S57_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L58_MS63_0nM_AB46-S58_A/2019-01-03-181105L58_MS63_0nM_AB46-S58_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L58_MS63_0nM_AB46-S58_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L59_MS63_10nM_AB46-S59_A/2019-01-03-181105L59_MS63_10nM_AB46-S59_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L59_MS63_10nM_AB46-S59_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L60_MS63_30nM_AB46-S60_A/2019-01-03-181105L60_MS63_30nM_AB46-S60_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L60_MS63_30nM_AB46-S60_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L61_MS1_AB47-S61_A/2019-01-03-181105L61_MS1_AB47-S61_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L61_MS1_AB47-S61_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L62_MS80_AB47-S62_A/2019-01-03-181105L62_MS80_AB47-S62_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L62_MS80_AB47-S62_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L63_MS81_AB47-S63_A/2019-01-03-181105L63_MS81_AB47-S63_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L63_MS81_AB47-S63_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L64_MS63_0nM_AB47-S64_A/2019-01-03-181105L64_MS63_0nM_AB47-S64_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L64_MS63_0nM_AB47-S64_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L65_MS63_10nM_AB47-S65_A/2019-01-03-181105L65_MS63_10nM_AB47-S65_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L65_MS63_10nM_AB47-S65_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L66_MS63_30nM_AB47-S66_A/2019-01-03-181105L66_MS63_30nM_AB47-S66_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L66_MS63_30nM_AB47-S66_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L67_MS1_AB48-S67_A/2019-01-03-181105L67_MS1_AB48-S67_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L67_MS1_AB48-S67_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L68_MS80_AB48-S68_A/2019-01-03-181105L68_MS80_AB48-S68_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L68_MS80_AB48-S68_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L69_MS81_AB48-S69_A/2019-01-03-181105L69_MS81_AB48-S69_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L69_MS81_AB48-S69_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L70_MS63_0nM_AB48-S70_A/2019-01-03-181105L70_MS63_0nM_AB48-S70_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L70_MS63_0nM_AB48-S70_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L71_MS63_10nM_AB48-S71_A/2019-01-03-181105L71_MS63_10nM_AB48-S71_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L71_MS63_10nM_AB48-S71_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L72_MS63_30nM_AB48-S72_A/2019-01-03-181105L72_MS63_30nM_AB48-S72_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes-merged.2019-01-03-181105L72_MS63_30nM_AB48-S72_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L01_MS1_input/2019-03-13-181105L01_MS1_input.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 genes-merged.2019-03-13-181105L01_MS1_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L02_MS80_input/2019-03-13-181105L02_MS80_input.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 genes-merged.2019-03-13-181105L02_MS80_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L03_MS81_input/2019-03-13-181105L03_MS81_input.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 genes-merged.2019-03-13-181105L03_MS81_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L04_MS63_0nM_input/2019-03-13-181105L04_MS63_0nM_input.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 genes-merged.2019-03-13-181105L04_MS63_0nM_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L05_MS63_10nM_input/2019-03-13-181105L05_MS63_10nM_input.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 genes-merged.2019-03-13-181105L05_MS63_10nM_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L06_MS63_30nM_input/2019-03-13-181105L06_MS63_30nM_input.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 genes-merged.2019-03-13-181105L06_MS63_30nM_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L07_MS1_AB20-H3/2019-03-13-190204L07_MS1_AB20-H3.2x36mers.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 genes-merged.2019-03-13-190204L07_MS1_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L08_MS80_AB20-H3/2019-03-13-190204L08_MS80_AB20-H3.2x36mers.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 genes-merged.2019-03-13-190204L08_MS80_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L09_MS81_AB20-H3/2019-03-13-190204L09_MS81_AB20-H3.2x36mers.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 genes-merged.2019-03-13-190204L09_MS81_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L10_MS63_0nM_AB20-H3/2019-03-13-190204L10_MS63_0nM_AB20-H3.2x36mers.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 genes-merged.2019-03-13-190204L10_MS63_0nM_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L11_MS63_10nM_AB20-H3/2019-03-13-190204L11_MS63_10nM_AB20-H3.2x36mers.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 genes-merged.2019-03-13-190204L11_MS63_10nM_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L12_MS63_30nM_AB20-H3/2019-03-13-190204L12_MS63_30nM_AB20-H3.2x36mers.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 genes-merged.2019-03-13-190204L12_MS63_30nM_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L13_MS1_AB21-H4/2019-03-13-190204L13_MS1_AB21-H4.2x36mers.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 genes-merged.2019-03-13-190204L13_MS1_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L14_MS80_AB21-H4/2019-03-13-190204L14_MS80_AB21-H4.2x36mers.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 genes-merged.2019-03-13-190204L14_MS80_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L15_MS81_AB21-H4/2019-03-13-190204L15_MS81_AB21-H4.2x36mers.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 genes-merged.2019-03-13-190204L15_MS81_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L16_MS63_0nM_AB21-H4/2019-03-13-190204L16_MS63_0nM_AB21-H4.2x36mers.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 genes-merged.2019-03-13-190204L16_MS63_0nM_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L17_MS63_10nM_AB21-H4/2019-03-13-190204L17_MS63_10nM_AB21-H4.2x36mers.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 genes-merged.2019-03-13-190204L17_MS63_10nM_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L18_MS63_30nM_AB21-H4/2019-03-13-190204L18_MS63_30nM_AB21-H4.2x36mers.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 genes-merged.2019-03-13-190204L18_MS63_30nM_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L19_MS1_AB36-H3K9ac/2019-03-13-190204L19_MS1_AB36-H3K9ac.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 genes-merged.2019-03-13-190204L19_MS1_AB36-H3K9ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L20_MS80_AB36-H3K9ac/2019-03-13-190204L20_MS80_AB36-H3K9ac.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 genes-merged.2019-03-13-190204L20_MS80_AB36-H3K9ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L21_MS81_AB36-H3K9ac/2019-03-13-190204L21_MS81_AB36-H3K9ac.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 genes-merged.2019-03-13-190204L21_MS81_AB36-H3K9ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac/2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac.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 genes-merged.2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac/2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac.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 genes-merged.2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac/2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac.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 genes-merged.2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L25_MS1_AB37-H3K18ac/2019-03-13-190204L25_MS1_AB37-H3K18ac.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 genes-merged.2019-03-13-190204L25_MS1_AB37-H3K18ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L26_MS80_AB37-H3K18ac/2019-03-13-190204L26_MS80_AB37-H3K18ac.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 genes-merged.2019-03-13-190204L26_MS80_AB37-H3K18ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L27_MS81_AB37-H3K18ac/2019-03-13-190204L27_MS81_AB37-H3K18ac.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 genes-merged.2019-03-13-190204L27_MS81_AB37-H3K18ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac/2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac.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 genes-merged.2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac/2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac.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 genes-merged.2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac/2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac.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 genes-merged.2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L31_MS1_AB38-H3K27ac/2019-03-13-190204L31_MS1_AB38-H3K27ac.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 genes-merged.2019-03-13-190204L31_MS1_AB38-H3K27ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L32_MS80_AB38-H3K27ac/2019-03-13-190204L32_MS80_AB38-H3K27ac.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 genes-merged.2019-03-13-190204L32_MS80_AB38-H3K27ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L33_MS81_AB38-H3K27ac/2019-03-13-190204L33_MS81_AB38-H3K27ac.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 genes-merged.2019-03-13-190204L33_MS81_AB38-H3K27ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac/2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac.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 genes-merged.2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac/2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac.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 genes-merged.2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac/2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac.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 genes-merged.2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L37_MS1_AB40-H4K16ac/2019-03-13-190204L37_MS1_AB40-H4K16ac.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 genes-merged.2019-03-13-190204L37_MS1_AB40-H4K16ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L38_MS80_AB40-H4K16ac/2019-03-13-190204L38_MS80_AB40-H4K16ac.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 genes-merged.2019-03-13-190204L38_MS80_AB40-H4K16ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L39_MS81_AB40-H4K16ac/2019-03-13-190204L39_MS81_AB40-H4K16ac.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 genes-merged.2019-03-13-190204L39_MS81_AB40-H4K16ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac/2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac.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 genes-merged.2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac/2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac.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 genes-merged.2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac/2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac.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 genes-merged.2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L43_MS1_AB46-H4K79me3/2019-03-13-190204L43_MS1_AB46-H4K79me3.2x36mers.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 genes-merged.2019-03-13-190204L43_MS1_AB46-H4K79me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L44_MS80_AB46-H4K79me3/2019-03-13-190204L44_MS80_AB46-H4K79me3.2x36mers.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 genes-merged.2019-03-13-190204L44_MS80_AB46-H4K79me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L45_MS81_AB46-H4K79me3/2019-03-13-190204L45_MS81_AB46-H4K79me3.2x36mers.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 genes-merged.2019-03-13-190204L45_MS81_AB46-H4K79me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3/2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3.2x36mers.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 genes-merged.2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3/2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3.2x36mers.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 genes-merged.2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3/2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3.2x36mers.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 genes-merged.2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L49_MS1_AB48-H4K36me3/2019-03-13-190204L49_MS1_AB48-H4K36me3.2x36mers.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 genes-merged.2019-03-13-190204L49_MS1_AB48-H4K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L50_MS80_AB48-H4K36me3/2019-03-13-190204L50_MS80_AB48-H4K36me3.2x36mers.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 genes-merged.2019-03-13-190204L50_MS80_AB48-H4K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L51_MS81_AB48-H4K36me3/2019-03-13-190204L51_MS81_AB48-H4K36me3.2x36mers.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 genes-merged.2019-03-13-190204L51_MS81_AB48-H4K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3/2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3.2x36mers.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 genes-merged.2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3/2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3.2x36mers.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 genes-merged.2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3/2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3.2x36mers.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 genes-merged.2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4/2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.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 genes-merged.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4/2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.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 genes-merged.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD/2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.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 genes-merged.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD/2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.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 genes-merged.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD/2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.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 genes-merged.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD/2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.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 genes-merged.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD/2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.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 genes-merged.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD/2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.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 genes-merged.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P/2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.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 genes-merged.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P/2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.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 genes-merged.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P/2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.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 genes-merged.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P/2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.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 genes-merged.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P/2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.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 genes-merged.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P/2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.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 genes-merged.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L01_MS212-MS99-DMSO_input/2019-04-06-190307-L01_MS212-MS99-DMSO_input.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 genes-merged.2019-04-06-190307-L01_MS212-MS99-DMSO_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L02_MS212-MS99-RAPA_input/2019-04-06-190307-L02_MS212-MS99-RAPA_input.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 genes-merged.2019-04-06-190307-L02_MS212-MS99-RAPA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L03_MS213-MS99-DMSO_input/2019-04-06-190307-L03_MS213-MS99-DMSO_input.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 genes-merged.2019-04-06-190307-L03_MS213-MS99-DMSO_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L04_MS213-MS99-RAPA_input/2019-04-06-190307-L04_MS213-MS99-RAPA_input.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 genes-merged.2019-04-06-190307-L04_MS213-MS99-RAPA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L05_MS63-MS99-00nM_input/2019-04-06-190307-L05_MS63-MS99-00nM_input.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 genes-merged.2019-04-06-190307-L05_MS63-MS99-00nM_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L06_MS63-MS99-30nM_input/2019-04-06-190307-L06_MS63-MS99-30nM_input.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 genes-merged.2019-04-06-190307-L06_MS63-MS99-30nM_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3/2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.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 genes-merged.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3/2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.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 genes-merged.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3/2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.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 genes-merged.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3/2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.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 genes-merged.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3/2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.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 genes-merged.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3/2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.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 genes-merged.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4/2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.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 genes-merged.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4/2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.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 genes-merged.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4/2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.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 genes-merged.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4/2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.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 genes-merged.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L01_MK555/2019-06-03-190429L01_MK555.2x36mers.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 genes-merged.2019-06-03-190429L01_MK555.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L03_MK645/2019-06-03-190429L03_MK645.2x36mers.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 genes-merged.2019-06-03-190429L03_MK645.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L04_MK653/2019-06-03-190429L04_MK653.2x36mers.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 genes-merged.2019-06-03-190429L04_MK653.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L05_MK554.2/2019-06-03-190429L05_MK554.2.2x36mers.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 genes-merged.2019-06-03-190429L05_MK554.2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L06_MK637/2019-06-03-190429L06_MK637.2x36mers.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 genes-merged.2019-06-03-190429L06_MK637.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L07_MK627/2019-06-03-190429L07_MK627.2x36mers.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 genes-merged.2019-06-03-190429L07_MK627.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L08_MK628/2019-06-03-190429L08_MK628.2x36mers.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 genes-merged.2019-06-03-190429L08_MK628.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L09_MK743/2019-06-03-190429L09_MK743.2x36mers.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 genes-merged.2019-06-03-190429L09_MK743.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L10_MK693/2019-06-03-190429L10_MK693.2x36mers.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 genes-merged.2019-06-03-190429L10_MK693.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L11_MK694/2019-06-03-190429L11_MK694.2x36mers.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 genes-merged.2019-06-03-190429L11_MK694.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L12_MK695/2019-06-03-190429L12_MK695.2x36mers.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 genes-merged.2019-06-03-190429L12_MK695.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L13_swi6del/2019-06-03-190429L13_swi6del.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 genes-merged.2019-06-03-190429L13_swi6del.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L01_MS207A_MS99_input/2019-06-03-190509L01_MS207A_MS99_input.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 genes-merged.2019-06-03-190509L01_MS207A_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L02_MS281_MS99_input/2019-06-03-190509L02_MS281_MS99_input.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 genes-merged.2019-06-03-190509L02_MS281_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L03_MS282_MS99_input/2019-06-03-190509L03_MS282_MS99_input.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 genes-merged.2019-06-03-190509L03_MS282_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L04_MS283_MS99_input/2019-06-03-190509L04_MS283_MS99_input.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 genes-merged.2019-06-03-190509L04_MS283_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L05_MS284_MS99_input/2019-06-03-190509L05_MS284_MS99_input.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 genes-merged.2019-06-03-190509L05_MS284_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L06_MS207B_MS99_input/2019-06-03-190509L06_MS207B_MS99_input.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 genes-merged.2019-06-03-190509L06_MS207B_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L07_MS285_MS99_input/2019-06-03-190509L07_MS285_MS99_input.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 genes-merged.2019-06-03-190509L07_MS285_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L08_MS286_MS99_input/2019-06-03-190509L08_MS286_MS99_input.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 genes-merged.2019-06-03-190509L08_MS286_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L09_MS287_MS99_input/2019-06-03-190509L09_MS287_MS99_input.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 genes-merged.2019-06-03-190509L09_MS287_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L10_MS288_MS99_input/2019-06-03-190509L10_MS288_MS99_input.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 genes-merged.2019-06-03-190509L10_MS288_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L11_MS207C_MS99_input/2019-06-03-190509L11_MS207C_MS99_input.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 genes-merged.2019-06-03-190509L11_MS207C_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L12_MS208_MS99_input/2019-06-03-190509L12_MS208_MS99_input.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 genes-merged.2019-06-03-190509L12_MS208_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L13_MS289_MS99_input/2019-06-03-190509L13_MS289_MS99_input.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 genes-merged.2019-06-03-190509L13_MS289_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L14_MS207A_MS99_AB1-Rpb1-CTD/2019-06-03-190509L14_MS207A_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L14_MS207A_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L15_MS281_MS99_AB1-Rpb1-CTD/2019-06-03-190509L15_MS281_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L15_MS281_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L16_MS282_MS99_AB1-Rpb1-CTD/2019-06-03-190509L16_MS282_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L16_MS282_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L17_MS283_MS99_AB1-Rpb1-CTD/2019-06-03-190509L17_MS283_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L17_MS283_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L18_MS284_MS99_AB1-Rpb1-CTD/2019-06-03-190509L18_MS284_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L18_MS284_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L19_MS207B_MS99_AB1-Rpb1-CTD/2019-06-03-190509L19_MS207B_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L19_MS207B_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L20_MS285_MS99_AB1-Rpb1-CTD/2019-06-03-190509L20_MS285_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L20_MS285_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L21_MS286_MS99_AB1-Rpb1-CTD/2019-06-03-190509L21_MS286_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L21_MS286_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L22_MS287_MS99_AB1-Rpb1-CTD/2019-06-03-190509L22_MS287_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L22_MS287_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L23_MS288_MS99_AB1-Rpb1-CTD/2019-06-03-190509L23_MS288_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L23_MS288_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L24_MS207C_MS99_AB1-Rpb1-CTD/2019-06-03-190509L24_MS207C_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L24_MS207C_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L25_MS208_MS99_AB1-Rpb1-CTD/2019-06-03-190509L25_MS208_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L25_MS208_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L26_MS289_MS99_AB1-Rpb1-CTD/2019-06-03-190509L26_MS289_MS99_AB1-Rpb1-CTD.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 genes-merged.2019-06-03-190509L26_MS289_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L27_MS207A_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L27_MS207A_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L27_MS207A_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L28_MS281_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L28_MS281_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L28_MS281_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L29_MS282_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L29_MS282_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L29_MS282_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L30_MS283_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L30_MS283_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L30_MS283_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L31_MS284_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L31_MS284_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L31_MS284_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L32_MS207B_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L32_MS207B_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L32_MS207B_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L33_MS285_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L33_MS285_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L33_MS285_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L34_MS286_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L34_MS286_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L34_MS286_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L35_MS287_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L35_MS287_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L35_MS287_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L36_MS288_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L36_MS288_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L36_MS288_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L37_MS207C_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L37_MS207C_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L37_MS207C_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L38_MS208_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L38_MS208_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L38_MS208_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L39_MS289_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L39_MS289_MS99_AB4-Rpb1-CTD-S2P.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 genes-merged.2019-06-03-190509L39_MS289_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L40_MS207A_MS99_AB20-H3/2019-06-03-190509L40_MS207A_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L40_MS207A_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L41_MS281_MS99_AB20-H3/2019-06-03-190509L41_MS281_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L41_MS281_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L42_MS282_MS99_AB20-H3/2019-06-03-190509L42_MS282_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L42_MS282_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L43_MS283_MS99_AB20-H3/2019-06-03-190509L43_MS283_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L43_MS283_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L44_MS284_MS99_AB20-H3/2019-06-03-190509L44_MS284_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L44_MS284_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L45_MS207B_MS99_AB20-H3/2019-06-03-190509L45_MS207B_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L45_MS207B_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L46_MS285_MS99_AB20-H3/2019-06-03-190509L46_MS285_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L46_MS285_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L47_MS286_MS99_AB20-H3/2019-06-03-190509L47_MS286_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L47_MS286_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L48_MS287_MS99_AB20-H3/2019-06-03-190509L48_MS287_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L48_MS287_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L49_MS288_MS99_AB20-H3/2019-06-03-190509L49_MS288_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L49_MS288_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L50_MS207C_MS99_AB20-H3/2019-06-03-190509L50_MS207C_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L50_MS207C_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L51_MS208_MS99_AB20-H3/2019-06-03-190509L51_MS208_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L51_MS208_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L52_MS289_MS99_AB20-H3/2019-06-03-190509L52_MS289_MS99_AB20-H3.2x36mers.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 genes-merged.2019-06-03-190509L52_MS289_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L53_MS207A_MS99_AB21-H4/2019-06-03-190509L53_MS207A_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L53_MS207A_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L54_MS281_MS99_AB21-H4/2019-06-03-190509L54_MS281_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L54_MS281_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L55_MS282_MS99_AB21-H4/2019-06-03-190509L55_MS282_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L55_MS282_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L56_MS283_MS99_AB21-H4/2019-06-03-190509L56_MS283_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L56_MS283_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L57_MS284_MS99_AB21-H4/2019-06-03-190509L57_MS284_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L57_MS284_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L58_MS207B_MS99_AB21-H4/2019-06-03-190509L58_MS207B_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L58_MS207B_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L59_MS285_MS99_AB21-H4/2019-06-03-190509L59_MS285_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L59_MS285_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L60_MS286_MS99_AB21-H4/2019-06-03-190509L60_MS286_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L60_MS286_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L61_MS287_MS99_AB21-H4/2019-06-03-190509L61_MS287_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L61_MS287_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L62_MS288_MS99_AB21-H4/2019-06-03-190509L62_MS288_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L62_MS288_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L63_MS207C_MS99_AB21-H4/2019-06-03-190509L63_MS207C_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L63_MS207C_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L64_MS208_MS99_AB21-H4/2019-06-03-190509L64_MS208_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L64_MS208_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L65_MS289_MS99_AB21-H4/2019-06-03-190509L65_MS289_MS99_AB21-H4.2x36mers.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 genes-merged.2019-06-03-190509L65_MS289_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L66_MS207A_MS99_AB48-H3K36me3/2019-06-03-190509L66_MS207A_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L66_MS207A_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L67_MS281_MS99_AB48-H3K36me3/2019-06-03-190509L67_MS281_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L67_MS281_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L68_MS282_MS99_AB48-H3K36me3/2019-06-03-190509L68_MS282_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L68_MS282_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L69_MS283_MS99_AB48-H3K36me3/2019-06-03-190509L69_MS283_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L69_MS283_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L70_MS284_MS99_AB48-H3K36me3/2019-06-03-190509L70_MS284_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L70_MS284_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L71_MS207B_MS99_AB48-H3K36me3/2019-06-03-190509L71_MS207B_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L71_MS207B_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L72_MS285_MS99_AB48-H3K36me3/2019-06-03-190509L72_MS285_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L72_MS285_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L73_MS286_MS99_AB48-H3K36me3/2019-06-03-190509L73_MS286_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L73_MS286_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L74_MS287_MS99_AB48-H3K36me3/2019-06-03-190509L74_MS287_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L74_MS287_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L75_MS288_MS99_AB48-H3K36me3/2019-06-03-190509L75_MS288_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L75_MS288_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L76_MS207C_MS99_AB48-H3K36me3/2019-06-03-190509L76_MS207C_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L76_MS207C_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L77_MS208_MS99_AB48-H3K36me3/2019-06-03-190509L77_MS208_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L77_MS208_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L78_MS289_MS99_AB48-H3K36me3/2019-06-03-190509L78_MS289_MS99_AB48-H3K36me3.2x36mers.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 genes-merged.2019-06-03-190509L78_MS289_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L01_MS207.1_input/2019-08-12-190722L01_MS207.1_input.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 genes-merged.2019-08-12-190722L01_MS207.1_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L02_MS208.1_input/2019-08-12-190722L02_MS208.1_input.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 genes-merged.2019-08-12-190722L02_MS208.1_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L03_MS281_input/2019-08-12-190722L03_MS281_input.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 genes-merged.2019-08-12-190722L03_MS281_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L04_MS282_input/2019-08-12-190722L04_MS282_input.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 genes-merged.2019-08-12-190722L04_MS282_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L05_MS283.1_input/2019-08-12-190722L05_MS283.1_input.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 genes-merged.2019-08-12-190722L05_MS283.1_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L06_MS284_input/2019-08-12-190722L06_MS284_input.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 genes-merged.2019-08-12-190722L06_MS284_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L07_MS285_input/2019-08-12-190722L07_MS285_input.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 genes-merged.2019-08-12-190722L07_MS285_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L08_MS289_input/2019-08-12-190722L08_MS289_input.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 genes-merged.2019-08-12-190722L08_MS289_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L09_MS207.2_input/2019-08-12-190722L09_MS207.2_input.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 genes-merged.2019-08-12-190722L09_MS207.2_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L10_MS208.2_input/2019-08-12-190722L10_MS208.2_input.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 genes-merged.2019-08-12-190722L10_MS208.2_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L11_MS209_input/2019-08-12-190722L11_MS209_input.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 genes-merged.2019-08-12-190722L11_MS209_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L12_MS289.2_input/2019-08-12-190722L12_MS289.2_input.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 genes-merged.2019-08-12-190722L12_MS289.2_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L13_MS207.1_AB20_H3/2019-08-12-190722L13_MS207.1_AB20_H3.2x36mers.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 genes-merged.2019-08-12-190722L13_MS207.1_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L14_MS208.1_AB20_H3/2019-08-12-190722L14_MS208.1_AB20_H3.2x36mers.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 genes-merged.2019-08-12-190722L14_MS208.1_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L15_MS281_AB20_H3/2019-08-12-190722L15_MS281_AB20_H3.2x36mers.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 genes-merged.2019-08-12-190722L15_MS281_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L16_MS282_AB20_H3/2019-08-12-190722L16_MS282_AB20_H3.2x36mers.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 genes-merged.2019-08-12-190722L16_MS282_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L17_MS283.1_AB20_H3/2019-08-12-190722L17_MS283.1_AB20_H3.2x36mers.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 genes-merged.2019-08-12-190722L17_MS283.1_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L18_MS284_AB20_H3/2019-08-12-190722L18_MS284_AB20_H3.2x36mers.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 genes-merged.2019-08-12-190722L18_MS284_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L19_MS285_AB20_H3/2019-08-12-190722L19_MS285_AB20_H3.2x36mers.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 genes-merged.2019-08-12-190722L19_MS285_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L20_MS289_AB20_H3/2019-08-12-190722L20_MS289_AB20_H3.2x36mers.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 genes-merged.2019-08-12-190722L20_MS289_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L21_MS207.2_AB20_H3/2019-08-12-190722L21_MS207.2_AB20_H3.2x36mers.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 genes-merged.2019-08-12-190722L21_MS207.2_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L22_MS208.2_AB20_H3/2019-08-12-190722L22_MS208.2_AB20_H3.2x36mers.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 genes-merged.2019-08-12-190722L22_MS208.2_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L23_MS209_AB20_H3/2019-08-12-190722L23_MS209_AB20_H3.2x36mers.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 genes-merged.2019-08-12-190722L23_MS209_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L24_MS289.2_AB20_H3/2019-08-12-190722L24_MS289.2_AB20_H3.2x36mers.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 genes-merged.2019-08-12-190722L24_MS289.2_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L25_MS207.1_AB21_H4/2019-08-12-190722L25_MS207.1_AB21_H4.2x36mers.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 genes-merged.2019-08-12-190722L25_MS207.1_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L26_MS208.1_AB21_H4/2019-08-12-190722L26_MS208.1_AB21_H4.2x36mers.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 genes-merged.2019-08-12-190722L26_MS208.1_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L27_MS281_AB21_H4/2019-08-12-190722L27_MS281_AB21_H4.2x36mers.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 genes-merged.2019-08-12-190722L27_MS281_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L28_MS282_AB21_H4/2019-08-12-190722L28_MS282_AB21_H4.2x36mers.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 genes-merged.2019-08-12-190722L28_MS282_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L29_MS283.1_AB21_H4/2019-08-12-190722L29_MS283.1_AB21_H4.2x36mers.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 genes-merged.2019-08-12-190722L29_MS283.1_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L30_MS284_AB21_H4/2019-08-12-190722L30_MS284_AB21_H4.2x36mers.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 genes-merged.2019-08-12-190722L30_MS284_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L31_MS285_AB21_H4/2019-08-12-190722L31_MS285_AB21_H4.2x36mers.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 genes-merged.2019-08-12-190722L31_MS285_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L32_MS289_AB21_H4/2019-08-12-190722L32_MS289_AB21_H4.2x36mers.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 genes-merged.2019-08-12-190722L32_MS289_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L33_MS207.2_AB21_H4/2019-08-12-190722L33_MS207.2_AB21_H4.2x36mers.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 genes-merged.2019-08-12-190722L33_MS207.2_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L34_MS208.2_AB21_H4/2019-08-12-190722L34_MS208.2_AB21_H4.2x36mers.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 genes-merged.2019-08-12-190722L34_MS208.2_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L35_MS209_AB21_H4/2019-08-12-190722L35_MS209_AB21_H4.2x36mers.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 genes-merged.2019-08-12-190722L35_MS209_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L36_MS289.2_AB21_H4/2019-08-12-190722L36_MS289.2_AB21_H4.2x36mers.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 genes-merged.2019-08-12-190722L36_MS289.2_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L37_MS207.1_AB01_Rpb1/2019-08-12-190722L37_MS207.1_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L37_MS207.1_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L38_MS208.1_AB01_Rpb1/2019-08-12-190722L38_MS208.1_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L38_MS208.1_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L39_MS281_AB01_Rpb1/2019-08-12-190722L39_MS281_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L39_MS281_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L40_MS282_AB01_Rpb1/2019-08-12-190722L40_MS282_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L40_MS282_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L41_MS283.1_AB01_Rpb1/2019-08-12-190722L41_MS283.1_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L41_MS283.1_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L42_MS284_AB01_Rpb1/2019-08-12-190722L42_MS284_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L42_MS284_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L43_MS285_AB01_Rpb1/2019-08-12-190722L43_MS285_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L43_MS285_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L44_MS289_AB01_Rpb1/2019-08-12-190722L44_MS289_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L44_MS289_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L45_MS207.2_AB01_Rpb1/2019-08-12-190722L45_MS207.2_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L45_MS207.2_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L46_MS208.2_AB01_Rpb1/2019-08-12-190722L46_MS208.2_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L46_MS208.2_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L47_MS209_AB01_Rpb1/2019-08-12-190722L47_MS209_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L47_MS209_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L48_MS289.2_AB01_Rpb1/2019-08-12-190722L48_MS289.2_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L48_MS289.2_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L49_MS207.1_AB04_Rpb1-S2P/2019-08-12-190722L49_MS207.1_AB04_Rpb1-S2P.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 genes-merged.2019-08-12-190722L49_MS207.1_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L50_MS208.1_AB04_Rpb1-S2P/2019-08-12-190722L50_MS208.1_AB04_Rpb1-S2P.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 genes-merged.2019-08-12-190722L50_MS208.1_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L51_MS281_AB04_Rpb1-S2P/2019-08-12-190722L51_MS281_AB04_Rpb1-S2P.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 genes-merged.2019-08-12-190722L51_MS281_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L52_MS282_AB04_Rpb1-S2P/2019-08-12-190722L52_MS282_AB04_Rpb1-S2P.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 genes-merged.2019-08-12-190722L52_MS282_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L53_MS283.1_AB04_Rpb1-S2P/2019-08-12-190722L53_MS283.1_AB04_Rpb1-S2P.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 genes-merged.2019-08-12-190722L53_MS283.1_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L54_MS284_AB04_Rpb1-S2P/2019-08-12-190722L54_MS284_AB04_Rpb1-S2P.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 genes-merged.2019-08-12-190722L54_MS284_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L55_MS285_AB04_Rpb1-S2P/2019-08-12-190722L55_MS285_AB04_Rpb1-S2P.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 genes-merged.2019-08-12-190722L55_MS285_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L56_MS289_AB04_Rpb1-S2P/2019-08-12-190722L56_MS289_AB04_Rpb1-S2P.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 genes-merged.2019-08-12-190722L56_MS289_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L57_MS207.2_AB04_Rpb1-S2P/2019-08-12-190722L57_MS207.2_AB04_Rpb1-S2P.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 genes-merged.2019-08-12-190722L57_MS207.2_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L58_MS208.2_AB04_Rpb1-S2P/2019-08-12-190722L58_MS208.2_AB04_Rpb1-S2P.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 genes-merged.2019-08-12-190722L58_MS208.2_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L59_MS209_AB04_Rpb1-S2P/2019-08-12-190722L59_MS209_AB04_Rpb1-S2P.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 genes-merged.2019-08-12-190722L59_MS209_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L60_MS289.2_AB04_Rpb1-S2P/2019-08-12-190722L60_MS289.2_AB04_Rpb1-S2P.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 genes-merged.2019-08-12-190722L60_MS289.2_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L61_MS207.2_AB01_Rpb1_RA/2019-08-12-190722L61_MS207.2_AB01_Rpb1_RA.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 genes-merged.2019-08-12-190722L61_MS207.2_AB01_Rpb1_RA.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L62_MS207.2_AB01_Rpb1_RB/2019-08-12-190722L62_MS207.2_AB01_Rpb1_RB.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 genes-merged.2019-08-12-190722L62_MS207.2_AB01_Rpb1_RB.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L63_MS289.2_AB01_Rpb1_RA/2019-08-12-190722L63_MS289.2_AB01_Rpb1_RA.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 genes-merged.2019-08-12-190722L63_MS289.2_AB01_Rpb1_RA.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L64_MS28.29_AB01_Rpb1_RB/2019-08-12-190722L64_MS28.29_AB01_Rpb1_RB.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 genes-merged.2019-08-12-190722L64_MS28.29_AB01_Rpb1_RB.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L65_MS521_AB101_GFP-NLS-V5/2019-08-12-190722L65_MS521_AB101_GFP-NLS-V5.2x36mers.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 genes-merged.2019-08-12-190722L65_MS521_AB101_GFP-NLS-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L66_MS529_AB101_WHI5-V5/2019-08-12-190722L66_MS529_AB101_WHI5-V5.2x36mers.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 genes-merged.2019-08-12-190722L66_MS529_AB101_WHI5-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L67_MS527_AB101_STB1-V5/2019-08-12-190722L67_MS527_AB101_STB1-V5.2x36mers.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 genes-merged.2019-08-12-190722L67_MS527_AB101_STB1-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L68_MS522_AB101_SWI4-V5/2019-08-12-190722L68_MS522_AB101_SWI4-V5.2x36mers.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 genes-merged.2019-08-12-190722L68_MS522_AB101_SWI4-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L69_MS524_AB101_SWI6-V5/2019-08-12-190722L69_MS524_AB101_SWI6-V5.2x36mers.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 genes-merged.2019-08-12-190722L69_MS524_AB101_SWI6-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L70_MS528_AB101_BCK2-V5/2019-08-12-190722L70_MS528_AB101_BCK2-V5.2x36mers.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 genes-merged.2019-08-12-190722L70_MS528_AB101_BCK2-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L71_MS523_AB101_MBP1-V5/2019-08-12-190722L71_MS523_AB101_MBP1-V5.2x36mers.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 genes-merged.2019-08-12-190722L71_MS523_AB101_MBP1-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L72_MS283.1_AB01_Rpb1/2019-08-12-190722L72_MS283.1_AB01_Rpb1.2x36mers.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 genes-merged.2019-08-12-190722L72_MS283.1_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L17_MS207.1-RAPA_AB1-Rpb1/2019-08-28-MS190729L17_MS207.1-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L17_MS207.1-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L18_MS208.1-RAPA_AB1-Rpb1/2019-08-28-MS190729L18_MS208.1-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L18_MS208.1-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L19_MS281-RAPA_AB1-Rpb1/2019-08-28-MS190729L19_MS281-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L19_MS281-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L20_MS282-RAPA_AB1-Rpb1/2019-08-28-MS190729L20_MS282-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L20_MS282-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L21_MS283.1-RAPA_AB1-Rpb1/2019-08-28-MS190729L21_MS283.1-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L21_MS283.1-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L22_MS284-RAPA_AB1-Rpb1/2019-08-28-MS190729L22_MS284-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L22_MS284-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L23_MS285-RAPA_AB1-Rpb1/2019-08-28-MS190729L23_MS285-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L23_MS285-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L24_MS289.1-RAPA_AB1-Rpb1/2019-08-28-MS190729L24_MS289.1-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L24_MS289.1-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L25_MS207.2-RAPA_AB1-Rpb1/2019-08-28-MS190729L25_MS207.2-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L25_MS207.2-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L26_MS208.2-RAPA_AB1-Rpb1/2019-08-28-MS190729L26_MS208.2-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L26_MS208.2-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L27_MS209-RAPA_AB1-Rpb1/2019-08-28-MS190729L27_MS209-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L27_MS209-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L28_MS283.2-RAPA_AB1-Rpb1/2019-08-28-MS190729L28_MS283.2-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L28_MS283.2-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L29_MS286-RAPA_AB1-Rpb1/2019-08-28-MS190729L29_MS286-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L29_MS286-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L30_MS287-RAPA_AB1-Rpb1/2019-08-28-MS190729L30_MS287-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L30_MS287-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L31_MS288-RAPA_AB1-Rpb1/2019-08-28-MS190729L31_MS288-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L31_MS288-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L32_MS289.2-RAPA_AB1-Rpb1/2019-08-28-MS190729L32_MS289.2-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L32_MS289.2-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L33_MS207-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L33_MS207-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L33_MS207-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L34_MS208-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L34_MS208-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L34_MS208-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L35_MS281-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L35_MS281-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L35_MS281-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L36_MS282-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L36_MS282-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L36_MS282-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L37_MS283-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L37_MS283-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L37_MS283-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L38_MS284-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L38_MS284-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L38_MS284-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L39_MS285-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L39_MS285-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L39_MS285-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L40_MS289-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L40_MS289-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L40_MS289-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L41_MS207.2-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L41_MS207.2-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L41_MS207.2-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L42_MS208.2-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L42_MS208.2-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L42_MS208.2-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L43_MS209-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L43_MS209-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L43_MS209-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L44_MS283.2-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L44_MS283.2-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L44_MS283.2-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L45_MS286-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L45_MS286-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L45_MS286-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L46_MS287-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L46_MS287-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L46_MS287-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L47_MS288-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L47_MS288-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L47_MS288-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L48_MS289.2-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L48_MS289.2-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L48_MS289.2-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L49_MS207-RAPA_AB1-Rpb1/2019-08-28-MS190729L49_MS207-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L49_MS207-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L50_MS208-RAPA_AB1-Rpb1/2019-08-28-MS190729L50_MS208-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L50_MS208-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L51_MS282-RAPA_AB1-Rpb1/2019-08-28-MS190729L51_MS282-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L51_MS282-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L52_MS207.2-RAPA_AB1-Rpb1/2019-08-28-MS190729L52_MS207.2-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L52_MS207.2-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L53_MS208.2-RAPA_AB1-Rpb1/2019-08-28-MS190729L53_MS208.2-RAPA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190729L53_MS208.2-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L54_MS207-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L54_MS207-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L54_MS207-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L55_MS208-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L55_MS208-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L55_MS208-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L56_MS283-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L56_MS283-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L56_MS283-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L58_MS208.2-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L58_MS208.2-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L58_MS208.2-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L59_MS287-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L59_MS287-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L59_MS287-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L60_MS288-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L60_MS288-RAPA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190729L60_MS288-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L01_MS55_FrA_input/2019-08-28-MS190807L01_MS55_FrA_input.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 genes-merged.2019-08-28-MS190807L01_MS55_FrA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L02_MS55_FrB_input/2019-08-28-MS190807L02_MS55_FrB_input.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 genes-merged.2019-08-28-MS190807L02_MS55_FrB_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L03_MS55_FrC_input/2019-08-28-MS190807L03_MS55_FrC_input.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 genes-merged.2019-08-28-MS190807L03_MS55_FrC_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L04_MS55_FrD_input/2019-08-28-MS190807L04_MS55_FrD_input.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 genes-merged.2019-08-28-MS190807L04_MS55_FrD_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L05_MS55_FrE_input/2019-08-28-MS190807L05_MS55_FrE_input.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 genes-merged.2019-08-28-MS190807L05_MS55_FrE_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L06_MS55_FrF_input/2019-08-28-MS190807L06_MS55_FrF_input.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 genes-merged.2019-08-28-MS190807L06_MS55_FrF_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L07_MS55_FrA_AB1-Rpb1/2019-08-28-MS190807L07_MS55_FrA_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190807L07_MS55_FrA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L08_MS55_FrB_AB1-Rpb1/2019-08-28-MS190807L08_MS55_FrB_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190807L08_MS55_FrB_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L09_MS55_FrC_AB1-Rpb1/2019-08-28-MS190807L09_MS55_FrC_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190807L09_MS55_FrC_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L10_MS55_FrD_AB1-Rpb1/2019-08-28-MS190807L10_MS55_FrD_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190807L10_MS55_FrD_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L11_MS55_FrE_AB1-Rpb1/2019-08-28-MS190807L11_MS55_FrE_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190807L11_MS55_FrE_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L12_MS55_FrF_AB1-Rpb1/2019-08-28-MS190807L12_MS55_FrF_AB1-Rpb1.2x36mers.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 genes-merged.2019-08-28-MS190807L12_MS55_FrF_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L13_MS55_FrA_AB4-Rpb1-S2P/2019-08-28-MS190807L13_MS55_FrA_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190807L13_MS55_FrA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L14_MS55_FrB_AB4-Rpb1-S2P/2019-08-28-MS190807L14_MS55_FrB_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190807L14_MS55_FrB_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L15_MS55_FrC_AB4-Rpb1-S2P/2019-08-28-MS190807L15_MS55_FrC_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190807L15_MS55_FrC_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L16_MS55_FrD_AB4-Rpb1-S2P/2019-08-28-MS190807L16_MS55_FrD_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190807L16_MS55_FrD_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L17_MS55_FrE_AB4-Rpb1-S2P/2019-08-28-MS190807L17_MS55_FrE_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190807L17_MS55_FrE_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L18_MS55_FrF_AB4-Rpb1-S2P/2019-08-28-MS190807L18_MS55_FrF_AB4-Rpb1-S2P.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 genes-merged.2019-08-28-MS190807L18_MS55_FrF_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L50_MS55_FrC_input_R/2019-08-28-MS190807L50_MS55_FrC_input_R.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 genes-merged.2019-08-28-MS190807L50_MS55_FrC_input_R.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L51_MS55_FrE_input_R/2019-08-28-MS190807L51_MS55_FrE_input_R.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 genes-merged.2019-08-28-MS190807L51_MS55_FrE_input_R.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L52_MS55_FrF_input_R/2019-08-28-MS190807L52_MS55_FrF_input_R.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 genes-merged.2019-08-28-MS190807L52_MS55_FrF_input_R.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L01_MS55_A_input/2019-10-07-190923L01_MS55_A_input.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 genes-merged.2019-10-07-190923L01_MS55_A_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L02_MS55_B_input/2019-10-07-190923L02_MS55_B_input.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 genes-merged.2019-10-07-190923L02_MS55_B_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L03_MS55_C_input/2019-10-07-190923L03_MS55_C_input.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 genes-merged.2019-10-07-190923L03_MS55_C_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L04_MS55_D_input/2019-10-07-190923L04_MS55_D_input.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 genes-merged.2019-10-07-190923L04_MS55_D_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L05_MS55_E_input/2019-10-07-190923L05_MS55_E_input.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 genes-merged.2019-10-07-190923L05_MS55_E_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L06_MS55_F_input/2019-10-07-190923L06_MS55_F_input.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 genes-merged.2019-10-07-190923L06_MS55_F_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L07_MS55_A_AB01-Rpb1/2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.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 genes-merged.2019-10-07-190923L07_MS55_A_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L08_MS55_B_AB01-Rpb1/2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.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 genes-merged.2019-10-07-190923L08_MS55_B_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L09_MS55_C_AB01-Rpb1/2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.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 genes-merged.2019-10-07-190923L09_MS55_C_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L10_MS55_D_AB01-Rpb1/2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.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 genes-merged.2019-10-07-190923L10_MS55_D_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L11_MS55_E_AB01-Rpb1/2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.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 genes-merged.2019-10-07-190923L11_MS55_E_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L12_MS55_F_AB01-Rpb1/2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.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 genes-merged.2019-10-07-190923L12_MS55_F_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P/2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.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 genes-merged.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P/2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.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 genes-merged.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P/2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.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 genes-merged.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P/2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.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 genes-merged.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P/2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.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 genes-merged.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P/2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.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 genes-merged.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L19_MS55_A_AB20-H3/2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.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 genes-merged.2019-10-07-190923L19_MS55_A_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L20_MS55_B_AB20-H3/2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.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 genes-merged.2019-10-07-190923L20_MS55_B_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L21_MS55_C_AB20-H3/2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.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 genes-merged.2019-10-07-190923L21_MS55_C_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L22_MS55_D_AB20-H3/2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.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 genes-merged.2019-10-07-190923L22_MS55_D_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L23_MS55_E_AB20-H3/2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.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 genes-merged.2019-10-07-190923L23_MS55_E_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L24_MS55_F_AB20-H3/2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.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 genes-merged.2019-10-07-190923L24_MS55_F_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L25_MS55_A_AB21-H4/2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.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 genes-merged.2019-10-07-190923L25_MS55_A_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L26_MS55_B_AB21-H4/2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.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 genes-merged.2019-10-07-190923L26_MS55_B_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L27_MS55_C_AB21-H4/2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.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 genes-merged.2019-10-07-190923L27_MS55_C_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L28_MS55_D_AB21-H4/2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.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 genes-merged.2019-10-07-190923L28_MS55_D_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L29_MS55_E_AB21-H4/2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.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 genes-merged.2019-10-07-190923L29_MS55_E_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L30_MS55_F_AB21-H4/2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.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 genes-merged.2019-10-07-190923L30_MS55_F_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L31_MS55_A_AB48-H3K36me3/2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.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 genes-merged.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L32_MS55_B_AB48-H3K36me3/2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.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 genes-merged.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L33_MS55_C_AB48-H3K36me3/2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.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 genes-merged.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L34_MS55_D_AB48-H3K36me3/2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.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 genes-merged.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L35_MS55_E_AB48-H3K36me3/2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.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 genes-merged.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L36_MS55_F_AB48-H3K36me3/2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.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 genes-merged.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L55_MS283.2_input/2019-10-07-190923L55_MS283.2_input.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 genes-merged.2019-10-07-190923L55_MS283.2_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L56_MS286_input/2019-10-07-190923L56_MS286_input.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 genes-merged.2019-10-07-190923L56_MS286_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L57_MS287_input/2019-10-07-190923L57_MS287_input.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 genes-merged.2019-10-07-190923L57_MS287_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L58_MS288_input/2019-10-07-190923L58_MS288_input.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 genes-merged.2019-10-07-190923L58_MS288_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L59_MS88_FrA_input/2019-10-07-190923L59_MS88_FrA_input.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 genes-merged.2019-10-07-190923L59_MS88_FrA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L60_MS88_FrB_input/2019-10-07-190923L60_MS88_FrB_input.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 genes-merged.2019-10-07-190923L60_MS88_FrB_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L61_MS88_FrC_input/2019-10-07-190923L61_MS88_FrC_input.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 genes-merged.2019-10-07-190923L61_MS88_FrC_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L62_MS88_FrD_input/2019-10-07-190923L62_MS88_FrD_input.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 genes-merged.2019-10-07-190923L62_MS88_FrD_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L63_MS88_FrA_AB01-Rpb1/2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.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 genes-merged.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L64_MS88_FrB_AB01-Rpb1/2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.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 genes-merged.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L65_MS88_FrC_AB01-Rpb1/2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.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 genes-merged.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L66_MS88_FrD_AB01-Rpb1/2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.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 genes-merged.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P/2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.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 genes-merged.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P/2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.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 genes-merged.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P/2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.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 genes-merged.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P/2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.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 genes-merged.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L71_MS88_FrA_AB20-H3/2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.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 genes-merged.2019-10-07-190923L71_MS88_FrA_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L72_MS88_FrB_AB20-H3/2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.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 genes-merged.2019-10-07-190923L72_MS88_FrB_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L73_MS88_FrC_AB20-H3/2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.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 genes-merged.2019-10-07-190923L73_MS88_FrC_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L74_MS88_FrD_AB20-H3/2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.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 genes-merged.2019-10-07-190923L74_MS88_FrD_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L75_MS88_FrA_AB21-H4/2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.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 genes-merged.2019-10-07-190923L75_MS88_FrA_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L76_MS88_FrB_AB21-H4/2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.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 genes-merged.2019-10-07-190923L76_MS88_FrB_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L77_MS88_FrC_AB21-H4/2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.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 genes-merged.2019-10-07-190923L77_MS88_FrC_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L78_MS88_FrD_AB21-H4/2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.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 genes-merged.2019-10-07-190923L78_MS88_FrD_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R/2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.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 genes-merged.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-A-YPD-input/2018-02-13-A-YPD-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-A-YPD-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-B-YPD-Pol2pS2/2018-02-13-B-YPD-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-B-YPD-Pol2pS2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-C-SCE_input/2018-02-13-C-SCE_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-C-SCE_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-D-SCE-Pol2pS2/2018-02-13-D-SCE-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-D-SCE-Pol2pS2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-E-SCE-H3/2018-02-13-E-SCE-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-E-SCE-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-F-SCE-CTD/2018-02-13-F-SCE-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-F-SCE-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-G-YPD-CTD/2018-02-13-G-YPD-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-G-YPD-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-H-SCD_noAA-input/2018-02-13-H-SCD_noAA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-H-SCD_noAA-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-I-SCD_Rpb1_AA-input/2018-02-13-I-SCD_Rpb1_AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-I-SCD_Rpb1_AA-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-J-SCD_TBP-AA-input/2018-02-13-J-SCD_TBP-AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-J-SCD_TBP-AA-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-K-SCD_noAA-H3/2018-02-13-K-SCD_noAA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-K-SCD_noAA-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-L-SCD_Rpb1_AA-H3/2018-02-13-L-SCD_Rpb1_AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-L-SCD_Rpb1_AA-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-M-SCD_TBP-AA-H3/2018-02-13-M-SCD_TBP-AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-M-SCD_TBP-AA-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-N-YPD-Rpb3/2018-02-13-N-YPD-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-N-YPD-Rpb3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-O-SCE-Rpb3/2018-02-13-O-SCE-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-O-SCE-Rpb3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-P-SCD_noAA-CTD/2018-02-13-P-SCD_noAA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-P-SCD_noAA-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-Q-SCD_Rpb1_AA-CTD/2018-02-13-Q-SCD_Rpb1_AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-Q-SCD_Rpb1_AA-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-R-SCD_TBP-AA-CTD/2018-02-13-R-SCD_TBP-AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-R-SCD_TBP-AA-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-S-SCD_noAA-Rpb3/2018-02-13-S-SCD_noAA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-S-SCD_noAA-Rpb3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-T-YPD-Pol2pS5_C/2018-02-13-T-YPD-Pol2pS5_C.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-T-YPD-Pol2pS5_C.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-U-YPD-Pol2pS5_D/2018-02-13-U-YPD-Pol2pS5_D.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-U-YPD-Pol2pS5_D.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-V-YPD-Pol2pS5_E/2018-02-13-V-YPD-Pol2pS5_E.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-V-YPD-Pol2pS5_E.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-W-SCD_Rpb1_AA-Rpb3/2018-02-13-W-SCD_Rpb1_AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-W-SCD_Rpb1_AA-Rpb3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-02-13-X-SCD_TBP-AA-Rpb3/2018-02-13-X-SCD_TBP-AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-02-13-X-SCD_TBP-AA-Rpb3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_0.0625/2018-04-20-H3-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-H3-SC_ratio_0.0625.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_0.25/2018-04-20-H3-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-H3-SC_ratio_0.25.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_0.5/2018-04-20-H3-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-H3-SC_ratio_0.5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_1/2018-04-20-H3-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-H3-SC_ratio_1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_16/2018-04-20-H3-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-H3-SC_ratio_16.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_2/2018-04-20-H3-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-H3-SC_ratio_2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-H3-SC_ratio_4/2018-04-20-H3-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-H3-SC_ratio_4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_0.0625/2018-04-20-Input-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Input-SC_ratio_0.0625.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_0.25/2018-04-20-Input-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Input-SC_ratio_0.25.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_0.5/2018-04-20-Input-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Input-SC_ratio_0.5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_1/2018-04-20-Input-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Input-SC_ratio_1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_16/2018-04-20-Input-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Input-SC_ratio_16.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_2/2018-04-20-Input-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Input-SC_ratio_2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Input-SC_ratio_4/2018-04-20-Input-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Input-SC_ratio_4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_0.0625/2018-04-20-Pol2pS2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2pS2-SC_ratio_0.0625.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_0.25/2018-04-20-Pol2pS2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2pS2-SC_ratio_0.25.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_0.5/2018-04-20-Pol2pS2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2pS2-SC_ratio_0.5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_1/2018-04-20-Pol2pS2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2pS2-SC_ratio_1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_16/2018-04-20-Pol2pS2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2pS2-SC_ratio_16.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_2/2018-04-20-Pol2pS2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2pS2-SC_ratio_2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS2-SC_ratio_4/2018-04-20-Pol2pS2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2pS2-SC_ratio_4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS5-L1/2018-04-20-Pol2pS5-L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2pS5-L1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS5-L2/2018-04-20-Pol2pS5-L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2pS5-L2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS5-L3/2018-04-20-Pol2pS5-L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2pS5-L3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2pS5-L4/2018-04-20-Pol2pS5-L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2pS5-L4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_0.0625/2018-04-20-Pol2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2-SC_ratio_0.0625.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_0.25/2018-04-20-Pol2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2-SC_ratio_0.25.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_0.5/2018-04-20-Pol2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2-SC_ratio_0.5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_1/2018-04-20-Pol2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2-SC_ratio_1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_16/2018-04-20-Pol2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2-SC_ratio_16.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_2/2018-04-20-Pol2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2-SC_ratio_2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-04-20-Pol2-SC_ratio_4/2018-04-20-Pol2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-04-20-Pol2-SC_ratio_4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-0nM-H3-180529_L13/2018-06-16-MS63-0nM-H3-180529_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-0nM-H3-180529_L13.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-0nM-Input-180529_L1/2018-06-16-MS63-0nM-Input-180529_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-0nM-Input-180529_L1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-0nM-Pol2-180529_L4/2018-06-16-MS63-0nM-Pol2-180529_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-0nM-Pol2-180529_L4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7/2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10/2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-10nM-H3-180529_L14/2018-06-16-MS63-10nM-H3-180529_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-10nM-H3-180529_L14.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-10nM-Input-180529_L2/2018-06-16-MS63-10nM-Input-180529_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-10nM-Input-180529_L2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-10nM-Pol2-180529_L5/2018-06-16-MS63-10nM-Pol2-180529_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-10nM-Pol2-180529_L5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8/2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11/2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-30nM-H3-180529_L15/2018-06-16-MS63-30nM-H3-180529_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-30nM-H3-180529_L15.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-30nM-Input-180529_L3/2018-06-16-MS63-30nM-Input-180529_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-30nM-Input-180529_L3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-30nM-Pol2-180529_L6/2018-06-16-MS63-30nM-Pol2-180529_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-30nM-Pol2-180529_L6.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9/2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12/2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS80-H3-180525_L14/2018-06-16-MS80-H3-180525_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS80-H3-180525_L14.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS80-Input-180525_L2/2018-06-16-MS80-Input-180525_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS80-Input-180525_L2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS80-Pol2-180525_L5/2018-06-16-MS80-Pol2-180525_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS80-Pol2-180525_L5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS80-RNAPII_pS2-180525_L8/2018-06-16-MS80-RNAPII_pS2-180525_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS80-RNAPII_pS2-180525_L8.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS80-RNAPII_pS5-180525_L11/2018-06-16-MS80-RNAPII_pS5-180525_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS80-RNAPII_pS5-180525_L11.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS81-H3-180525_L15/2018-06-16-MS81-H3-180525_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS81-H3-180525_L15.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS81-Input-180525_L3/2018-06-16-MS81-Input-180525_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS81-Input-180525_L3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS81-Pol2-180525_L6/2018-06-16-MS81-Pol2-180525_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS81-Pol2-180525_L6.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS81-RNAPII_pS2-180525_L9/2018-06-16-MS81-RNAPII_pS2-180525_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS81-RNAPII_pS2-180525_L9.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS81-RNAPII_pS5-180525_L12/2018-06-16-MS81-RNAPII_pS5-180525_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-MS81-RNAPII_pS5-180525_L12.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21/2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1/2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11/2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22/2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2/2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12/2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23/2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3/2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13/2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24/2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4/2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14/2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25/2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5/2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15/2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_0min_+rap-H3-180522_L26/2018-06-16-TBP_AA_0min_+rap-H3-180522_L26.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_0min_+rap-H3-180522_L26.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_0min_+rap-Input-180522_L6/2018-06-16-TBP_AA_0min_+rap-Input-180522_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_0min_+rap-Input-180522_L6.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16/2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_10min_+rap-H3-180522_L27/2018-06-16-TBP_AA_10min_+rap-H3-180522_L27.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_10min_+rap-H3-180522_L27.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_10min_+rap-Input-180522_L7/2018-06-16-TBP_AA_10min_+rap-Input-180522_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_10min_+rap-Input-180522_L7.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17/2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_20min_+rap-H3-180522_L28/2018-06-16-TBP_AA_20min_+rap-H3-180522_L28.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_20min_+rap-H3-180522_L28.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_20min_+rap-Input-180522_L8/2018-06-16-TBP_AA_20min_+rap-Input-180522_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_20min_+rap-Input-180522_L8.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18/2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_30min_+rap-H3-180522_L29/2018-06-16-TBP_AA_30min_+rap-H3-180522_L29.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_30min_+rap-H3-180522_L29.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_30min_+rap-Input-180522_L9/2018-06-16-TBP_AA_30min_+rap-Input-180522_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_30min_+rap-Input-180522_L9.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19/2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_60min_+rap-H3-180522_L30/2018-06-16-TBP_AA_60min_+rap-H3-180522_L30.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_60min_+rap-H3-180522_L30.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_60min_+rap-Input-180522_L10/2018-06-16-TBP_AA_60min_+rap-Input-180522_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_60min_+rap-Input-180522_L10.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20/2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-H3-180525_L13/2018-06-16-WT_OD_0.1-H3-180525_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.1-H3-180525_L13.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-H3-180531_L19/2018-06-16-WT_OD_0.1-H3-180531_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.1-H3-180531_L19.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-Input-180525_L1/2018-06-16-WT_OD_0.1-Input-180525_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.1-Input-180525_L1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-Input-180531_L1/2018-06-16-WT_OD_0.1-Input-180531_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.1-Input-180531_L1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-Pol2-180525_L4/2018-06-16-WT_OD_0.1-Pol2-180525_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.1-Pol2-180525_L4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-Pol2-180531_L7/2018-06-16-WT_OD_0.1-Pol2-180531_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.1-Pol2-180531_L7.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7/2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13/2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10/2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.2-H3-180531_L20/2018-06-16-WT_OD_0.2-H3-180531_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.2-H3-180531_L20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.2-Input-180531_L2/2018-06-16-WT_OD_0.2-Input-180531_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.2-Input-180531_L2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.2-Pol2-180531_L8/2018-06-16-WT_OD_0.2-Pol2-180531_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.2-Pol2-180531_L8.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14/2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.3-H3-180531_L21/2018-06-16-WT_OD_0.3-H3-180531_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.3-H3-180531_L21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.3-Input-180531_L3/2018-06-16-WT_OD_0.3-Input-180531_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.3-Input-180531_L3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.3-Pol2-180531_L9/2018-06-16-WT_OD_0.3-Pol2-180531_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.3-Pol2-180531_L9.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15/2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.4-H3-180531_L22/2018-06-16-WT_OD_0.4-H3-180531_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.4-H3-180531_L22.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.4-Input-180531_L4/2018-06-16-WT_OD_0.4-Input-180531_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.4-Input-180531_L4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.4-Pol2-180531_L10/2018-06-16-WT_OD_0.4-Pol2-180531_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.4-Pol2-180531_L10.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16/2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.5-H3-180531_L23/2018-06-16-WT_OD_0.5-H3-180531_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.5-H3-180531_L23.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.5-Input-180531_L5/2018-06-16-WT_OD_0.5-Input-180531_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.5-Input-180531_L5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.5-Pol2-180531_L11/2018-06-16-WT_OD_0.5-Pol2-180531_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.5-Pol2-180531_L11.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17/2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.6-H3-180531_L24/2018-06-16-WT_OD_0.6-H3-180531_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.6-H3-180531_L24.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.6-Input-180531_L6/2018-06-16-WT_OD_0.6-Input-180531_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.6-Input-180531_L6.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.6-Pol2-180531_L12/2018-06-16-WT_OD_0.6-Pol2-180531_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.6-Pol2-180531_L12.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18/2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS80_15-H3-rep1-whi5/2018-07-12-MS80_15-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-07-12-MS80_15-H3-rep1-whi5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS80_15-H3-rep2-whi5/2018-07-12-MS80_15-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-07-12-MS80_15-H3-rep2-whi5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS80_15-input-whi5/2018-07-12-MS80_15-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-07-12-MS80_15-input-whi5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS80_5-H3-rep1-whi5/2018-07-12-MS80_5-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-07-12-MS80_5-H3-rep1-whi5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS80_5-H3-rep2-whi5/2018-07-12-MS80_5-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-07-12-MS80_5-H3-rep2-whi5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS80_5-input-whi5/2018-07-12-MS80_5-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-07-12-MS80_5-input-whi5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS81_15-H3-rep1-cln3/2018-07-12-MS81_15-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-07-12-MS81_15-H3-rep1-cln3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS81_15-H3-rep2-cln3/2018-07-12-MS81_15-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-07-12-MS81_15-H3-rep2-cln3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS81_15-input-cln3/2018-07-12-MS81_15-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-07-12-MS81_15-input-cln3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS81_5-H3-rep1-cln3/2018-07-12-MS81_5-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-07-12-MS81_5-H3-rep1-cln3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS81_5-H3-rep2-cln3/2018-07-12-MS81_5-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-07-12-MS81_5-H3-rep2-cln3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-07-12-MS81_5-input-cln3/2018-07-12-MS81_5-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-07-12-MS81_5-input-cln3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L10-MS80-AB21/2018-09-13-180718-L10-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L10-MS80-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L11-MS81-input/2018-09-13-180718-L11-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L11-MS81-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L12-MS81-input-2/2018-09-13-180718-L12-MS81-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L12-MS81-input-2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L13-MS81-AB5/2018-09-13-180718-L13-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L13-MS81-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L14-MS81-AB20/2018-09-13-180718-L14-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L14-MS81-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L15-MS81-AB21/2018-09-13-180718-L15-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L15-MS81-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L16-MS63-0nM-input/2018-09-13-180718-L16-MS63-0nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L16-MS63-0nM-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L17-MS63-0nM-input-2/2018-09-13-180718-L17-MS63-0nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L17-MS63-0nM-input-2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L18-MS63-0nM-AB5/2018-09-13-180718-L18-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L18-MS63-0nM-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L19-MS63-0nM-AB20/2018-09-13-180718-L19-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L19-MS63-0nM-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L1-MS1-input/2018-09-13-180718-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L1-MS1-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L20-MS63-0nM-AB21/2018-09-13-180718-L20-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L20-MS63-0nM-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L21-MS63-10nM-input/2018-09-13-180718-L21-MS63-10nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L21-MS63-10nM-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L22-MS63-10nM-input-2/2018-09-13-180718-L22-MS63-10nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L22-MS63-10nM-input-2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L23-MS63-10nM-AB5/2018-09-13-180718-L23-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L23-MS63-10nM-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L24-MS63-10nM-AB20/2018-09-13-180718-L24-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L24-MS63-10nM-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L25-MS63-10nM-AB21/2018-09-13-180718-L25-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L25-MS63-10nM-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L26-MS63-30nM-input/2018-09-13-180718-L26-MS63-30nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L26-MS63-30nM-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L27-MS63-30nM-input-2/2018-09-13-180718-L27-MS63-30nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L27-MS63-30nM-input-2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L28-MS63-30nM-AB5/2018-09-13-180718-L28-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L28-MS63-30nM-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L29-MS63-30nM-AB20/2018-09-13-180718-L29-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L29-MS63-30nM-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L2-MS1-input-2/2018-09-13-180718-L2-MS1-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L2-MS1-input-2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L30-MS63-30nM-AB21/2018-09-13-180718-L30-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L30-MS63-30nM-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L3-MS1-AB5/2018-09-13-180718-L3-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L3-MS1-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L4-MS1-AB20/2018-09-13-180718-L4-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L4-MS1-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L5-MS1-AB21/2018-09-13-180718-L5-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L5-MS1-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L6-MS80-input/2018-09-13-180718-L6-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L6-MS80-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L7-MS80-input-2/2018-09-13-180718-L7-MS80-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L7-MS80-input-2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L8-MS80-AB5/2018-09-13-180718-L8-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L8-MS80-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180718-L9-MS80-AB20/2018-09-13-180718-L9-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180718-L9-MS80-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L10-MS63-10nM-AB5/2018-09-13-180723-L10-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L10-MS63-10nM-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L11-MS63-10nM-AB20/2018-09-13-180723-L11-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L11-MS63-10nM-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L12-MS63-10nM-AB21/2018-09-13-180723-L12-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L12-MS63-10nM-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L13-MS63-30nM-input2/2018-09-13-180723-L13-MS63-30nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L13-MS63-30nM-input2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L14-MS63-30nM-AB1/2018-09-13-180723-L14-MS63-30nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L14-MS63-30nM-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L15-MS63-30nM-AB4/2018-09-13-180723-L15-MS63-30nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L15-MS63-30nM-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L16-MS63-30nM-AB5/2018-09-13-180723-L16-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L16-MS63-30nM-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L17-MS63-30nM-AB20/2018-09-13-180723-L17-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L17-MS63-30nM-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L18-MS63-30nM-AB21/2018-09-13-180723-L18-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L18-MS63-30nM-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L1-MS63-0nM-input1/2018-09-13-180723-L1-MS63-0nM-input1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L1-MS63-0nM-input1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L2-MS63-0nM-AB1/2018-09-13-180723-L2-MS63-0nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L2-MS63-0nM-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L3-MS63-0nM-AB4/2018-09-13-180723-L3-MS63-0nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L3-MS63-0nM-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L4-MS63-0nM-AB5/2018-09-13-180723-L4-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L4-MS63-0nM-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L5-MS63-0nM-AB20/2018-09-13-180723-L5-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L5-MS63-0nM-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L6-MS63-0nM-AB21/2018-09-13-180723-L6-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L6-MS63-0nM-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L7-MS63-10nM-input2/2018-09-13-180723-L7-MS63-10nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L7-MS63-10nM-input2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L8-MS63-10nM-AB1/2018-09-13-180723-L8-MS63-10nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L8-MS63-10nM-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180723-L9-MS63-10nM-AB4/2018-09-13-180723-L9-MS63-10nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180723-L9-MS63-10nM-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L10-MS80-AB5/2018-09-13-180731-L10-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L10-MS80-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L11-MS80-AB20/2018-09-13-180731-L11-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L11-MS80-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L12-MS80-AB21/2018-09-13-180731-L12-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L12-MS80-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L13-MS81-input/2018-09-13-180731-L13-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L13-MS81-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L14-MS81-AB1/2018-09-13-180731-L14-MS81-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L14-MS81-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L15-MS81-AB4/2018-09-13-180731-L15-MS81-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L15-MS81-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L16-MS81-AB5/2018-09-13-180731-L16-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L16-MS81-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L17-MS81-AB20/2018-09-13-180731-L17-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L17-MS81-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L18-MS81-AB21/2018-09-13-180731-L18-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L18-MS81-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L19-MS55-1-input/2018-09-13-180731-L19-MS55-1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L19-MS55-1-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L1-MS1-input/2018-09-13-180731-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L1-MS1-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L20-MS55-1-AB1/2018-09-13-180731-L20-MS55-1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L20-MS55-1-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L21-MS55-1-AB4/2018-09-13-180731-L21-MS55-1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L21-MS55-1-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L22-MS55-1-AB5/2018-09-13-180731-L22-MS55-1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L22-MS55-1-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L23-MS55-1-AB20/2018-09-13-180731-L23-MS55-1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L23-MS55-1-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L24-MS55-1-AB21/2018-09-13-180731-L24-MS55-1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L24-MS55-1-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L25-MS55-2-input/2018-09-13-180731-L25-MS55-2-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L25-MS55-2-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L26-MS55-2-AB1/2018-09-13-180731-L26-MS55-2-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L26-MS55-2-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L27-MS55-2-AB4/2018-09-13-180731-L27-MS55-2-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L27-MS55-2-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L28-MS55-2-AB5/2018-09-13-180731-L28-MS55-2-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L28-MS55-2-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L29-MS55-2-AB20/2018-09-13-180731-L29-MS55-2-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L29-MS55-2-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L2-MS1-AB1/2018-09-13-180731-L2-MS1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L2-MS1-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L30-MS55-2-AB21/2018-09-13-180731-L30-MS55-2-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L30-MS55-2-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L31-MS55-3-input/2018-09-13-180731-L31-MS55-3-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L31-MS55-3-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L32-MS55-3-AB1/2018-09-13-180731-L32-MS55-3-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L32-MS55-3-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L33-MS55-3-AB4/2018-09-13-180731-L33-MS55-3-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L33-MS55-3-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L34-MS55-3-AB5/2018-09-13-180731-L34-MS55-3-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L34-MS55-3-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L35-MS55-3-AB20/2018-09-13-180731-L35-MS55-3-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L35-MS55-3-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L36-MS55-3-AB21/2018-09-13-180731-L36-MS55-3-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L36-MS55-3-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L37-MS55-4-input/2018-09-13-180731-L37-MS55-4-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L37-MS55-4-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L38-MS55-4-AB1/2018-09-13-180731-L38-MS55-4-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L38-MS55-4-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L39-MS55-4-AB4/2018-09-13-180731-L39-MS55-4-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L39-MS55-4-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L3-MS1-AB4/2018-09-13-180731-L3-MS1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L3-MS1-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L40-MS55-4-AB5/2018-09-13-180731-L40-MS55-4-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L40-MS55-4-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L41-MS55-4-AB20/2018-09-13-180731-L41-MS55-4-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L41-MS55-4-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L42-MS55-4-AB21/2018-09-13-180731-L42-MS55-4-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L42-MS55-4-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L4-MS1-AB5/2018-09-13-180731-L4-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L4-MS1-AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L5-MS1-AB20/2018-09-13-180731-L5-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L5-MS1-AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L6-MS1-AB21/2018-09-13-180731-L6-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L6-MS1-AB21.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L7-MS80-input/2018-09-13-180731-L7-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L7-MS80-input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L8-MS80-AB1/2018-09-13-180731-L8-MS80-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L8-MS80-AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-09-13-180731-L9-MS80-AB4/2018-09-13-180731-L9-MS80-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-09-13-180731-L9-MS80-AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20/2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s1-1-180917_L01_MS230_DMSO_input/2018-10-14-s1-1-180917_L01_MS230_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s1-1-180917_L01_MS230_DMSO_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s11-3-180917_L11_MS232_DMSO_input/2018-10-14-s11-3-180917_L11_MS232_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s11-3-180917_L11_MS232_DMSO_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1/2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4/2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5/2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20/2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s16-4-180917_L16_MS230_RAPA_input/2018-10-14-s16-4-180917_L16_MS230_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s16-4-180917_L16_MS230_RAPA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1/2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4/2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5/2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20/2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1/2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s21-5-180917_L21_MS231_RAPA_input/2018-10-14-s21-5-180917_L21_MS231_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s21-5-180917_L21_MS231_RAPA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1/2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4/2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5/2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20/2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s26-6-180917_L26_MS232_RAPA_input/2018-10-14-s26-6-180917_L26_MS232_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s26-6-180917_L26_MS232_RAPA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1/2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4/2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5/2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20/2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4/2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s76-23-180821_L01_MS1_input/2018-10-14-s76-23-180821_L01_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s76-23-180821_L01_MS1_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s77-23-180821_L02_MS1_AB20/2018-10-14-s77-23-180821_L02_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s77-23-180821_L02_MS1_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s78-23-180821_L03_MS1_AB39/2018-10-14-s78-23-180821_L03_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s78-23-180821_L03_MS1_AB39.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s79-23-180821_L04_MS1_AB42/2018-10-14-s79-23-180821_L04_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s79-23-180821_L04_MS1_AB42.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s80-23-180821_L05_MS1_AB43/2018-10-14-s80-23-180821_L05_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s80-23-180821_L05_MS1_AB43.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s81-23-180821_L06_MS1_AB44/2018-10-14-s81-23-180821_L06_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s81-23-180821_L06_MS1_AB44.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4/2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s82-23-180821_L07_MS1_AB45/2018-10-14-s82-23-180821_L07_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s82-23-180821_L07_MS1_AB45.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s83-23-180821_L08_MS1_AB46/2018-10-14-s83-23-180821_L08_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s83-23-180821_L08_MS1_AB46.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s84-23-180821_L09_MS1_AB47/2018-10-14-s84-23-180821_L09_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s84-23-180821_L09_MS1_AB47.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s85-23-180821_L10_MS1_AB48/2018-10-14-s85-23-180821_L10_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s85-23-180821_L10_MS1_AB48.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s86-24-180827_L1_MS1_input/2018-10-14-s86-24-180827_L1_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s86-24-180827_L1_MS1_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s87-24-180827_L2_MS1_AB20/2018-10-14-s87-24-180827_L2_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s87-24-180827_L2_MS1_AB20.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s88-24-180827_L3_MS1_AB39/2018-10-14-s88-24-180827_L3_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s88-24-180827_L3_MS1_AB39.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s89-24-180827_L4_MS1_AB41/2018-10-14-s89-24-180827_L4_MS1_AB41.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s89-24-180827_L4_MS1_AB41.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s90-24-180827_L5_MS1_AB42/2018-10-14-s90-24-180827_L5_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s90-24-180827_L5_MS1_AB42.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s91-24-180827_L6_MS1_AB43/2018-10-14-s91-24-180827_L6_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s91-24-180827_L6_MS1_AB43.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5/2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s92-24-180827_L7_MS1_AB44/2018-10-14-s92-24-180827_L7_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s92-24-180827_L7_MS1_AB44.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s93-24-180827_L8_MS1_AB45/2018-10-14-s93-24-180827_L8_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s93-24-180827_L8_MS1_AB45.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s94-24-180827_L9_MS1_AB46/2018-10-14-s94-24-180827_L9_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s94-24-180827_L9_MS1_AB46.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s95-24-180827_L10_MS1_AB47/2018-10-14-s95-24-180827_L10_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s95-24-180827_L10_MS1_AB47.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s96-24-180827_L11_MS1_AB48/2018-10-14-s96-24-180827_L11_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2018-10-14-s96-24-180827_L11_MS1_AB48.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L01_MS1_input-S01_A/2019-01-03-181105L01_MS1_input-S01_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L01_MS1_input-S01_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L02_MS80_input-S02_A/2019-01-03-181105L02_MS80_input-S02_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L02_MS80_input-S02_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L03_MS81_input-S03_A/2019-01-03-181105L03_MS81_input-S03_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L03_MS81_input-S03_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L04_MS63_0nM_input-S04_A/2019-01-03-181105L04_MS63_0nM_input-S04_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L04_MS63_0nM_input-S04_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L05_MS63_10nM_input-S05_A/2019-01-03-181105L05_MS63_10nM_input-S05_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L05_MS63_10nM_input-S05_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L06_MS63_30nM_input-S06_A/2019-01-03-181105L06_MS63_30nM_input-S06_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L06_MS63_30nM_input-S06_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L07_MS1_AB20-S07_A/2019-01-03-181105L07_MS1_AB20-S07_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L07_MS1_AB20-S07_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L08_MS80_AB20-S08_A/2019-01-03-181105L08_MS80_AB20-S08_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L08_MS80_AB20-S08_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L09_MS81_AB20-S09_A/2019-01-03-181105L09_MS81_AB20-S09_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L09_MS81_AB20-S09_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L10_MS63_0nM_AB20-S10_A/2019-01-03-181105L10_MS63_0nM_AB20-S10_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L10_MS63_0nM_AB20-S10_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L11_MS63_10nM_AB20-S11_A/2019-01-03-181105L11_MS63_10nM_AB20-S11_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L11_MS63_10nM_AB20-S11_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L12_MS63_30nM_AB20-S12_A/2019-01-03-181105L12_MS63_30nM_AB20-S12_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L12_MS63_30nM_AB20-S12_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L13_MS1_AB21-S13_A/2019-01-03-181105L13_MS1_AB21-S13_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L13_MS1_AB21-S13_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L14_MS80_AB21-S14_A/2019-01-03-181105L14_MS80_AB21-S14_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L14_MS80_AB21-S14_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L15_MS81_AB21-S15_A/2019-01-03-181105L15_MS81_AB21-S15_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L15_MS81_AB21-S15_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L16_MS63_0nM_AB21-S16_A/2019-01-03-181105L16_MS63_0nM_AB21-S16_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L16_MS63_0nM_AB21-S16_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L17_MS63_10nM_AB21-S17_A/2019-01-03-181105L17_MS63_10nM_AB21-S17_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L17_MS63_10nM_AB21-S17_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L18_MS63_30nM_AB21-S18_A/2019-01-03-181105L18_MS63_30nM_AB21-S18_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L18_MS63_30nM_AB21-S18_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L19_MS1_AB39-S19_A/2019-01-03-181105L19_MS1_AB39-S19_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L19_MS1_AB39-S19_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L20_MS80_AB39-S20_A/2019-01-03-181105L20_MS80_AB39-S20_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L20_MS80_AB39-S20_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L21_MS81_AB39-S21_A/2019-01-03-181105L21_MS81_AB39-S21_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L21_MS81_AB39-S21_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L22_MS63_0nM_AB39-S22_A/2019-01-03-181105L22_MS63_0nM_AB39-S22_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L22_MS63_0nM_AB39-S22_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L23_MS63_10nM_AB39-S23_A/2019-01-03-181105L23_MS63_10nM_AB39-S23_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L23_MS63_10nM_AB39-S23_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L24_MS63_30nM_AB39-S24_A/2019-01-03-181105L24_MS63_30nM_AB39-S24_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L24_MS63_30nM_AB39-S24_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L25_MS1_AB41-S25_A/2019-01-03-181105L25_MS1_AB41-S25_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L25_MS1_AB41-S25_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L26_MS80_AB41-S26_A/2019-01-03-181105L26_MS80_AB41-S26_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L26_MS80_AB41-S26_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L27_MS81_AB41-S27_A/2019-01-03-181105L27_MS81_AB41-S27_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L27_MS81_AB41-S27_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L28_MS63_0nM_AB41-S28_A/2019-01-03-181105L28_MS63_0nM_AB41-S28_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L28_MS63_0nM_AB41-S28_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L29_MS63_10nM_AB41-S29_A/2019-01-03-181105L29_MS63_10nM_AB41-S29_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L29_MS63_10nM_AB41-S29_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L30_MS63_30nM_AB41-S30_A/2019-01-03-181105L30_MS63_30nM_AB41-S30_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L30_MS63_30nM_AB41-S30_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L31_MS1_AB42-S31_A/2019-01-03-181105L31_MS1_AB42-S31_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L31_MS1_AB42-S31_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L32_MS80_AB42-S32_A/2019-01-03-181105L32_MS80_AB42-S32_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L32_MS80_AB42-S32_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L33_MS81_AB42-S33_A/2019-01-03-181105L33_MS81_AB42-S33_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L33_MS81_AB42-S33_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L34_MS63_0nM_AB42-S34_A/2019-01-03-181105L34_MS63_0nM_AB42-S34_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L34_MS63_0nM_AB42-S34_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L35_MS63_10nM_AB42-S35_A/2019-01-03-181105L35_MS63_10nM_AB42-S35_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L35_MS63_10nM_AB42-S35_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L36_MS63_30nM_AB42-S36_A/2019-01-03-181105L36_MS63_30nM_AB42-S36_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L36_MS63_30nM_AB42-S36_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L37_MS1_AB43-S37_A/2019-01-03-181105L37_MS1_AB43-S37_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L37_MS1_AB43-S37_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L38_MS80_AB43-S38_A/2019-01-03-181105L38_MS80_AB43-S38_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L38_MS80_AB43-S38_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L39_MS81_AB43-S39_A/2019-01-03-181105L39_MS81_AB43-S39_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L39_MS81_AB43-S39_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L40_MS63_0nM_AB43-S40_A/2019-01-03-181105L40_MS63_0nM_AB43-S40_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L40_MS63_0nM_AB43-S40_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L41_MS63_10nM_AB43-S41_A/2019-01-03-181105L41_MS63_10nM_AB43-S41_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L41_MS63_10nM_AB43-S41_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L42_MS63_30nM_AB43-S42_A/2019-01-03-181105L42_MS63_30nM_AB43-S42_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L42_MS63_30nM_AB43-S42_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L43_MS1_AB44-S43_A/2019-01-03-181105L43_MS1_AB44-S43_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L43_MS1_AB44-S43_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L44_MS80_AB44-S44_A/2019-01-03-181105L44_MS80_AB44-S44_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L44_MS80_AB44-S44_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L45_MS81_AB44-S45_A/2019-01-03-181105L45_MS81_AB44-S45_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L45_MS81_AB44-S45_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L46_MS63_0nM_AB44-S46_A/2019-01-03-181105L46_MS63_0nM_AB44-S46_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L46_MS63_0nM_AB44-S46_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L47_MS63_10nM_AB44-S47_A/2019-01-03-181105L47_MS63_10nM_AB44-S47_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L47_MS63_10nM_AB44-S47_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L48_MS63_30nM_AB44-S48_A/2019-01-03-181105L48_MS63_30nM_AB44-S48_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L48_MS63_30nM_AB44-S48_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L49_MS1_AB45-S49_A/2019-01-03-181105L49_MS1_AB45-S49_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L49_MS1_AB45-S49_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L50_MS80_AB45-S50_A/2019-01-03-181105L50_MS80_AB45-S50_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L50_MS80_AB45-S50_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L51_MS81_AB45-S51_A/2019-01-03-181105L51_MS81_AB45-S51_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L51_MS81_AB45-S51_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L52_MS63_0nM_AB45-S52_A/2019-01-03-181105L52_MS63_0nM_AB45-S52_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L52_MS63_0nM_AB45-S52_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L53_MS63_10nM_AB45-S53_A/2019-01-03-181105L53_MS63_10nM_AB45-S53_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L53_MS63_10nM_AB45-S53_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L54_MS63_30nM_AB45-S54_A/2019-01-03-181105L54_MS63_30nM_AB45-S54_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L54_MS63_30nM_AB45-S54_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L55_MS1_AB46-S55_A/2019-01-03-181105L55_MS1_AB46-S55_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L55_MS1_AB46-S55_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L56_MS80_AB46-S56_A/2019-01-03-181105L56_MS80_AB46-S56_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L56_MS80_AB46-S56_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L57_MS81_AB46-S57_A/2019-01-03-181105L57_MS81_AB46-S57_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L57_MS81_AB46-S57_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L58_MS63_0nM_AB46-S58_A/2019-01-03-181105L58_MS63_0nM_AB46-S58_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L58_MS63_0nM_AB46-S58_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L59_MS63_10nM_AB46-S59_A/2019-01-03-181105L59_MS63_10nM_AB46-S59_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L59_MS63_10nM_AB46-S59_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L60_MS63_30nM_AB46-S60_A/2019-01-03-181105L60_MS63_30nM_AB46-S60_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L60_MS63_30nM_AB46-S60_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L61_MS1_AB47-S61_A/2019-01-03-181105L61_MS1_AB47-S61_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L61_MS1_AB47-S61_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L62_MS80_AB47-S62_A/2019-01-03-181105L62_MS80_AB47-S62_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L62_MS80_AB47-S62_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L63_MS81_AB47-S63_A/2019-01-03-181105L63_MS81_AB47-S63_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L63_MS81_AB47-S63_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L64_MS63_0nM_AB47-S64_A/2019-01-03-181105L64_MS63_0nM_AB47-S64_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L64_MS63_0nM_AB47-S64_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L65_MS63_10nM_AB47-S65_A/2019-01-03-181105L65_MS63_10nM_AB47-S65_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L65_MS63_10nM_AB47-S65_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L66_MS63_30nM_AB47-S66_A/2019-01-03-181105L66_MS63_30nM_AB47-S66_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L66_MS63_30nM_AB47-S66_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L67_MS1_AB48-S67_A/2019-01-03-181105L67_MS1_AB48-S67_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L67_MS1_AB48-S67_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L68_MS80_AB48-S68_A/2019-01-03-181105L68_MS80_AB48-S68_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L68_MS80_AB48-S68_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L69_MS81_AB48-S69_A/2019-01-03-181105L69_MS81_AB48-S69_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L69_MS81_AB48-S69_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L70_MS63_0nM_AB48-S70_A/2019-01-03-181105L70_MS63_0nM_AB48-S70_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L70_MS63_0nM_AB48-S70_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L71_MS63_10nM_AB48-S71_A/2019-01-03-181105L71_MS63_10nM_AB48-S71_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L71_MS63_10nM_AB48-S71_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L72_MS63_30nM_AB48-S72_A/2019-01-03-181105L72_MS63_30nM_AB48-S72_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp-merged.2019-01-03-181105L72_MS63_30nM_AB48-S72_A.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L01_MS1_input/2019-03-13-181105L01_MS1_input.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 TSS-250bp-350bp-merged.2019-03-13-181105L01_MS1_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L02_MS80_input/2019-03-13-181105L02_MS80_input.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 TSS-250bp-350bp-merged.2019-03-13-181105L02_MS80_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L03_MS81_input/2019-03-13-181105L03_MS81_input.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 TSS-250bp-350bp-merged.2019-03-13-181105L03_MS81_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L04_MS63_0nM_input/2019-03-13-181105L04_MS63_0nM_input.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 TSS-250bp-350bp-merged.2019-03-13-181105L04_MS63_0nM_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L05_MS63_10nM_input/2019-03-13-181105L05_MS63_10nM_input.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 TSS-250bp-350bp-merged.2019-03-13-181105L05_MS63_10nM_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L06_MS63_30nM_input/2019-03-13-181105L06_MS63_30nM_input.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 TSS-250bp-350bp-merged.2019-03-13-181105L06_MS63_30nM_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L07_MS1_AB20-H3/2019-03-13-190204L07_MS1_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L07_MS1_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L08_MS80_AB20-H3/2019-03-13-190204L08_MS80_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L08_MS80_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L09_MS81_AB20-H3/2019-03-13-190204L09_MS81_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L09_MS81_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L10_MS63_0nM_AB20-H3/2019-03-13-190204L10_MS63_0nM_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L10_MS63_0nM_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L11_MS63_10nM_AB20-H3/2019-03-13-190204L11_MS63_10nM_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L11_MS63_10nM_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L12_MS63_30nM_AB20-H3/2019-03-13-190204L12_MS63_30nM_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L12_MS63_30nM_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L13_MS1_AB21-H4/2019-03-13-190204L13_MS1_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L13_MS1_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L14_MS80_AB21-H4/2019-03-13-190204L14_MS80_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L14_MS80_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L15_MS81_AB21-H4/2019-03-13-190204L15_MS81_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L15_MS81_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L16_MS63_0nM_AB21-H4/2019-03-13-190204L16_MS63_0nM_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L16_MS63_0nM_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L17_MS63_10nM_AB21-H4/2019-03-13-190204L17_MS63_10nM_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L17_MS63_10nM_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L18_MS63_30nM_AB21-H4/2019-03-13-190204L18_MS63_30nM_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L18_MS63_30nM_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L19_MS1_AB36-H3K9ac/2019-03-13-190204L19_MS1_AB36-H3K9ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L19_MS1_AB36-H3K9ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L20_MS80_AB36-H3K9ac/2019-03-13-190204L20_MS80_AB36-H3K9ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L20_MS80_AB36-H3K9ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L21_MS81_AB36-H3K9ac/2019-03-13-190204L21_MS81_AB36-H3K9ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L21_MS81_AB36-H3K9ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac/2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac/2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac/2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L25_MS1_AB37-H3K18ac/2019-03-13-190204L25_MS1_AB37-H3K18ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L25_MS1_AB37-H3K18ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L26_MS80_AB37-H3K18ac/2019-03-13-190204L26_MS80_AB37-H3K18ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L26_MS80_AB37-H3K18ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L27_MS81_AB37-H3K18ac/2019-03-13-190204L27_MS81_AB37-H3K18ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L27_MS81_AB37-H3K18ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac/2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac/2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac/2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L31_MS1_AB38-H3K27ac/2019-03-13-190204L31_MS1_AB38-H3K27ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L31_MS1_AB38-H3K27ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L32_MS80_AB38-H3K27ac/2019-03-13-190204L32_MS80_AB38-H3K27ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L32_MS80_AB38-H3K27ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L33_MS81_AB38-H3K27ac/2019-03-13-190204L33_MS81_AB38-H3K27ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L33_MS81_AB38-H3K27ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac/2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac/2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac/2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L37_MS1_AB40-H4K16ac/2019-03-13-190204L37_MS1_AB40-H4K16ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L37_MS1_AB40-H4K16ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L38_MS80_AB40-H4K16ac/2019-03-13-190204L38_MS80_AB40-H4K16ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L38_MS80_AB40-H4K16ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L39_MS81_AB40-H4K16ac/2019-03-13-190204L39_MS81_AB40-H4K16ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L39_MS81_AB40-H4K16ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac/2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac/2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac/2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac.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 TSS-250bp-350bp-merged.2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L43_MS1_AB46-H4K79me3/2019-03-13-190204L43_MS1_AB46-H4K79me3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L43_MS1_AB46-H4K79me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L44_MS80_AB46-H4K79me3/2019-03-13-190204L44_MS80_AB46-H4K79me3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L44_MS80_AB46-H4K79me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L45_MS81_AB46-H4K79me3/2019-03-13-190204L45_MS81_AB46-H4K79me3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L45_MS81_AB46-H4K79me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3/2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3/2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3/2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L49_MS1_AB48-H4K36me3/2019-03-13-190204L49_MS1_AB48-H4K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L49_MS1_AB48-H4K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L50_MS80_AB48-H4K36me3/2019-03-13-190204L50_MS80_AB48-H4K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L50_MS80_AB48-H4K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L51_MS81_AB48-H4K36me3/2019-03-13-190204L51_MS81_AB48-H4K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L51_MS81_AB48-H4K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3/2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3/2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3/2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4/2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4/2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD/2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.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 TSS-250bp-350bp-merged.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD/2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.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 TSS-250bp-350bp-merged.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD/2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.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 TSS-250bp-350bp-merged.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD/2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.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 TSS-250bp-350bp-merged.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD/2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.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 TSS-250bp-350bp-merged.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD/2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.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 TSS-250bp-350bp-merged.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P/2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.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 TSS-250bp-350bp-merged.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P/2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.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 TSS-250bp-350bp-merged.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P/2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.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 TSS-250bp-350bp-merged.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P/2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.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 TSS-250bp-350bp-merged.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P/2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.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 TSS-250bp-350bp-merged.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P/2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.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 TSS-250bp-350bp-merged.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L01_MS212-MS99-DMSO_input/2019-04-06-190307-L01_MS212-MS99-DMSO_input.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 TSS-250bp-350bp-merged.2019-04-06-190307-L01_MS212-MS99-DMSO_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L02_MS212-MS99-RAPA_input/2019-04-06-190307-L02_MS212-MS99-RAPA_input.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 TSS-250bp-350bp-merged.2019-04-06-190307-L02_MS212-MS99-RAPA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L03_MS213-MS99-DMSO_input/2019-04-06-190307-L03_MS213-MS99-DMSO_input.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 TSS-250bp-350bp-merged.2019-04-06-190307-L03_MS213-MS99-DMSO_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L04_MS213-MS99-RAPA_input/2019-04-06-190307-L04_MS213-MS99-RAPA_input.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 TSS-250bp-350bp-merged.2019-04-06-190307-L04_MS213-MS99-RAPA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L05_MS63-MS99-00nM_input/2019-04-06-190307-L05_MS63-MS99-00nM_input.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 TSS-250bp-350bp-merged.2019-04-06-190307-L05_MS63-MS99-00nM_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L06_MS63-MS99-30nM_input/2019-04-06-190307-L06_MS63-MS99-30nM_input.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 TSS-250bp-350bp-merged.2019-04-06-190307-L06_MS63-MS99-30nM_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3/2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3/2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3/2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3/2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3/2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3/2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4/2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4/2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4/2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4/2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L01_MK555/2019-06-03-190429L01_MK555.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190429L01_MK555.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L03_MK645/2019-06-03-190429L03_MK645.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190429L03_MK645.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L04_MK653/2019-06-03-190429L04_MK653.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190429L04_MK653.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L05_MK554.2/2019-06-03-190429L05_MK554.2.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190429L05_MK554.2.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L06_MK637/2019-06-03-190429L06_MK637.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190429L06_MK637.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L07_MK627/2019-06-03-190429L07_MK627.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190429L07_MK627.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L08_MK628/2019-06-03-190429L08_MK628.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190429L08_MK628.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L09_MK743/2019-06-03-190429L09_MK743.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190429L09_MK743.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L10_MK693/2019-06-03-190429L10_MK693.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190429L10_MK693.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L11_MK694/2019-06-03-190429L11_MK694.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190429L11_MK694.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L12_MK695/2019-06-03-190429L12_MK695.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190429L12_MK695.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190429L13_swi6del/2019-06-03-190429L13_swi6del.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 TSS-250bp-350bp-merged.2019-06-03-190429L13_swi6del.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L01_MS207A_MS99_input/2019-06-03-190509L01_MS207A_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L01_MS207A_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L02_MS281_MS99_input/2019-06-03-190509L02_MS281_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L02_MS281_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L03_MS282_MS99_input/2019-06-03-190509L03_MS282_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L03_MS282_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L04_MS283_MS99_input/2019-06-03-190509L04_MS283_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L04_MS283_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L05_MS284_MS99_input/2019-06-03-190509L05_MS284_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L05_MS284_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L06_MS207B_MS99_input/2019-06-03-190509L06_MS207B_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L06_MS207B_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L07_MS285_MS99_input/2019-06-03-190509L07_MS285_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L07_MS285_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L08_MS286_MS99_input/2019-06-03-190509L08_MS286_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L08_MS286_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L09_MS287_MS99_input/2019-06-03-190509L09_MS287_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L09_MS287_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L10_MS288_MS99_input/2019-06-03-190509L10_MS288_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L10_MS288_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L11_MS207C_MS99_input/2019-06-03-190509L11_MS207C_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L11_MS207C_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L12_MS208_MS99_input/2019-06-03-190509L12_MS208_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L12_MS208_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L13_MS289_MS99_input/2019-06-03-190509L13_MS289_MS99_input.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 TSS-250bp-350bp-merged.2019-06-03-190509L13_MS289_MS99_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L14_MS207A_MS99_AB1-Rpb1-CTD/2019-06-03-190509L14_MS207A_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L14_MS207A_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L15_MS281_MS99_AB1-Rpb1-CTD/2019-06-03-190509L15_MS281_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L15_MS281_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L16_MS282_MS99_AB1-Rpb1-CTD/2019-06-03-190509L16_MS282_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L16_MS282_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L17_MS283_MS99_AB1-Rpb1-CTD/2019-06-03-190509L17_MS283_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L17_MS283_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L18_MS284_MS99_AB1-Rpb1-CTD/2019-06-03-190509L18_MS284_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L18_MS284_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L19_MS207B_MS99_AB1-Rpb1-CTD/2019-06-03-190509L19_MS207B_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L19_MS207B_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L20_MS285_MS99_AB1-Rpb1-CTD/2019-06-03-190509L20_MS285_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L20_MS285_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L21_MS286_MS99_AB1-Rpb1-CTD/2019-06-03-190509L21_MS286_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L21_MS286_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L22_MS287_MS99_AB1-Rpb1-CTD/2019-06-03-190509L22_MS287_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L22_MS287_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L23_MS288_MS99_AB1-Rpb1-CTD/2019-06-03-190509L23_MS288_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L23_MS288_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L24_MS207C_MS99_AB1-Rpb1-CTD/2019-06-03-190509L24_MS207C_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L24_MS207C_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L25_MS208_MS99_AB1-Rpb1-CTD/2019-06-03-190509L25_MS208_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L25_MS208_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L26_MS289_MS99_AB1-Rpb1-CTD/2019-06-03-190509L26_MS289_MS99_AB1-Rpb1-CTD.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 TSS-250bp-350bp-merged.2019-06-03-190509L26_MS289_MS99_AB1-Rpb1-CTD.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L27_MS207A_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L27_MS207A_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L27_MS207A_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L28_MS281_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L28_MS281_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L28_MS281_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L29_MS282_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L29_MS282_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L29_MS282_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L30_MS283_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L30_MS283_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L30_MS283_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L31_MS284_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L31_MS284_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L31_MS284_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L32_MS207B_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L32_MS207B_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L32_MS207B_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L33_MS285_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L33_MS285_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L33_MS285_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L34_MS286_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L34_MS286_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L34_MS286_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L35_MS287_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L35_MS287_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L35_MS287_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L36_MS288_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L36_MS288_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L36_MS288_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L37_MS207C_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L37_MS207C_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L37_MS207C_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L38_MS208_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L38_MS208_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L38_MS208_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L39_MS289_MS99_AB4-Rpb1-CTD-S2P/2019-06-03-190509L39_MS289_MS99_AB4-Rpb1-CTD-S2P.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 TSS-250bp-350bp-merged.2019-06-03-190509L39_MS289_MS99_AB4-Rpb1-CTD-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L40_MS207A_MS99_AB20-H3/2019-06-03-190509L40_MS207A_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L40_MS207A_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L41_MS281_MS99_AB20-H3/2019-06-03-190509L41_MS281_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L41_MS281_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L42_MS282_MS99_AB20-H3/2019-06-03-190509L42_MS282_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L42_MS282_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L43_MS283_MS99_AB20-H3/2019-06-03-190509L43_MS283_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L43_MS283_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L44_MS284_MS99_AB20-H3/2019-06-03-190509L44_MS284_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L44_MS284_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L45_MS207B_MS99_AB20-H3/2019-06-03-190509L45_MS207B_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L45_MS207B_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L46_MS285_MS99_AB20-H3/2019-06-03-190509L46_MS285_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L46_MS285_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L47_MS286_MS99_AB20-H3/2019-06-03-190509L47_MS286_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L47_MS286_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L48_MS287_MS99_AB20-H3/2019-06-03-190509L48_MS287_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L48_MS287_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L49_MS288_MS99_AB20-H3/2019-06-03-190509L49_MS288_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L49_MS288_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L50_MS207C_MS99_AB20-H3/2019-06-03-190509L50_MS207C_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L50_MS207C_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L51_MS208_MS99_AB20-H3/2019-06-03-190509L51_MS208_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L51_MS208_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L52_MS289_MS99_AB20-H3/2019-06-03-190509L52_MS289_MS99_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L52_MS289_MS99_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L53_MS207A_MS99_AB21-H4/2019-06-03-190509L53_MS207A_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L53_MS207A_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L54_MS281_MS99_AB21-H4/2019-06-03-190509L54_MS281_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L54_MS281_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L55_MS282_MS99_AB21-H4/2019-06-03-190509L55_MS282_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L55_MS282_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L56_MS283_MS99_AB21-H4/2019-06-03-190509L56_MS283_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L56_MS283_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L57_MS284_MS99_AB21-H4/2019-06-03-190509L57_MS284_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L57_MS284_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L58_MS207B_MS99_AB21-H4/2019-06-03-190509L58_MS207B_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L58_MS207B_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L59_MS285_MS99_AB21-H4/2019-06-03-190509L59_MS285_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L59_MS285_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L60_MS286_MS99_AB21-H4/2019-06-03-190509L60_MS286_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L60_MS286_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L61_MS287_MS99_AB21-H4/2019-06-03-190509L61_MS287_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L61_MS287_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L62_MS288_MS99_AB21-H4/2019-06-03-190509L62_MS288_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L62_MS288_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L63_MS207C_MS99_AB21-H4/2019-06-03-190509L63_MS207C_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L63_MS207C_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L64_MS208_MS99_AB21-H4/2019-06-03-190509L64_MS208_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L64_MS208_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L65_MS289_MS99_AB21-H4/2019-06-03-190509L65_MS289_MS99_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L65_MS289_MS99_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L66_MS207A_MS99_AB48-H3K36me3/2019-06-03-190509L66_MS207A_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L66_MS207A_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L67_MS281_MS99_AB48-H3K36me3/2019-06-03-190509L67_MS281_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L67_MS281_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L68_MS282_MS99_AB48-H3K36me3/2019-06-03-190509L68_MS282_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L68_MS282_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L69_MS283_MS99_AB48-H3K36me3/2019-06-03-190509L69_MS283_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L69_MS283_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L70_MS284_MS99_AB48-H3K36me3/2019-06-03-190509L70_MS284_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L70_MS284_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L71_MS207B_MS99_AB48-H3K36me3/2019-06-03-190509L71_MS207B_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L71_MS207B_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L72_MS285_MS99_AB48-H3K36me3/2019-06-03-190509L72_MS285_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L72_MS285_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L73_MS286_MS99_AB48-H3K36me3/2019-06-03-190509L73_MS286_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L73_MS286_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L74_MS287_MS99_AB48-H3K36me3/2019-06-03-190509L74_MS287_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L74_MS287_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L75_MS288_MS99_AB48-H3K36me3/2019-06-03-190509L75_MS288_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L75_MS288_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L76_MS207C_MS99_AB48-H3K36me3/2019-06-03-190509L76_MS207C_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L76_MS207C_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L77_MS208_MS99_AB48-H3K36me3/2019-06-03-190509L77_MS208_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L77_MS208_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-06-03-190509L78_MS289_MS99_AB48-H3K36me3/2019-06-03-190509L78_MS289_MS99_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-06-03-190509L78_MS289_MS99_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L01_MS207.1_input/2019-08-12-190722L01_MS207.1_input.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 TSS-250bp-350bp-merged.2019-08-12-190722L01_MS207.1_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L02_MS208.1_input/2019-08-12-190722L02_MS208.1_input.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 TSS-250bp-350bp-merged.2019-08-12-190722L02_MS208.1_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L03_MS281_input/2019-08-12-190722L03_MS281_input.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 TSS-250bp-350bp-merged.2019-08-12-190722L03_MS281_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L04_MS282_input/2019-08-12-190722L04_MS282_input.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 TSS-250bp-350bp-merged.2019-08-12-190722L04_MS282_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L05_MS283.1_input/2019-08-12-190722L05_MS283.1_input.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 TSS-250bp-350bp-merged.2019-08-12-190722L05_MS283.1_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L06_MS284_input/2019-08-12-190722L06_MS284_input.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 TSS-250bp-350bp-merged.2019-08-12-190722L06_MS284_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L07_MS285_input/2019-08-12-190722L07_MS285_input.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 TSS-250bp-350bp-merged.2019-08-12-190722L07_MS285_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L08_MS289_input/2019-08-12-190722L08_MS289_input.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 TSS-250bp-350bp-merged.2019-08-12-190722L08_MS289_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L09_MS207.2_input/2019-08-12-190722L09_MS207.2_input.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 TSS-250bp-350bp-merged.2019-08-12-190722L09_MS207.2_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L10_MS208.2_input/2019-08-12-190722L10_MS208.2_input.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 TSS-250bp-350bp-merged.2019-08-12-190722L10_MS208.2_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L11_MS209_input/2019-08-12-190722L11_MS209_input.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 TSS-250bp-350bp-merged.2019-08-12-190722L11_MS209_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L12_MS289.2_input/2019-08-12-190722L12_MS289.2_input.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 TSS-250bp-350bp-merged.2019-08-12-190722L12_MS289.2_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L13_MS207.1_AB20_H3/2019-08-12-190722L13_MS207.1_AB20_H3.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L13_MS207.1_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L14_MS208.1_AB20_H3/2019-08-12-190722L14_MS208.1_AB20_H3.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L14_MS208.1_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L15_MS281_AB20_H3/2019-08-12-190722L15_MS281_AB20_H3.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L15_MS281_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L16_MS282_AB20_H3/2019-08-12-190722L16_MS282_AB20_H3.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L16_MS282_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L17_MS283.1_AB20_H3/2019-08-12-190722L17_MS283.1_AB20_H3.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L17_MS283.1_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L18_MS284_AB20_H3/2019-08-12-190722L18_MS284_AB20_H3.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L18_MS284_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L19_MS285_AB20_H3/2019-08-12-190722L19_MS285_AB20_H3.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L19_MS285_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L20_MS289_AB20_H3/2019-08-12-190722L20_MS289_AB20_H3.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L20_MS289_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L21_MS207.2_AB20_H3/2019-08-12-190722L21_MS207.2_AB20_H3.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L21_MS207.2_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L22_MS208.2_AB20_H3/2019-08-12-190722L22_MS208.2_AB20_H3.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L22_MS208.2_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L23_MS209_AB20_H3/2019-08-12-190722L23_MS209_AB20_H3.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L23_MS209_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L24_MS289.2_AB20_H3/2019-08-12-190722L24_MS289.2_AB20_H3.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L24_MS289.2_AB20_H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L25_MS207.1_AB21_H4/2019-08-12-190722L25_MS207.1_AB21_H4.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L25_MS207.1_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L26_MS208.1_AB21_H4/2019-08-12-190722L26_MS208.1_AB21_H4.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L26_MS208.1_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L27_MS281_AB21_H4/2019-08-12-190722L27_MS281_AB21_H4.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L27_MS281_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L28_MS282_AB21_H4/2019-08-12-190722L28_MS282_AB21_H4.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L28_MS282_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L29_MS283.1_AB21_H4/2019-08-12-190722L29_MS283.1_AB21_H4.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L29_MS283.1_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L30_MS284_AB21_H4/2019-08-12-190722L30_MS284_AB21_H4.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L30_MS284_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L31_MS285_AB21_H4/2019-08-12-190722L31_MS285_AB21_H4.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L31_MS285_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L32_MS289_AB21_H4/2019-08-12-190722L32_MS289_AB21_H4.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L32_MS289_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L33_MS207.2_AB21_H4/2019-08-12-190722L33_MS207.2_AB21_H4.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L33_MS207.2_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L34_MS208.2_AB21_H4/2019-08-12-190722L34_MS208.2_AB21_H4.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L34_MS208.2_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L35_MS209_AB21_H4/2019-08-12-190722L35_MS209_AB21_H4.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L35_MS209_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L36_MS289.2_AB21_H4/2019-08-12-190722L36_MS289.2_AB21_H4.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L36_MS289.2_AB21_H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L37_MS207.1_AB01_Rpb1/2019-08-12-190722L37_MS207.1_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L37_MS207.1_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L38_MS208.1_AB01_Rpb1/2019-08-12-190722L38_MS208.1_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L38_MS208.1_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L39_MS281_AB01_Rpb1/2019-08-12-190722L39_MS281_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L39_MS281_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L40_MS282_AB01_Rpb1/2019-08-12-190722L40_MS282_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L40_MS282_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L41_MS283.1_AB01_Rpb1/2019-08-12-190722L41_MS283.1_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L41_MS283.1_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L42_MS284_AB01_Rpb1/2019-08-12-190722L42_MS284_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L42_MS284_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L43_MS285_AB01_Rpb1/2019-08-12-190722L43_MS285_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L43_MS285_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L44_MS289_AB01_Rpb1/2019-08-12-190722L44_MS289_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L44_MS289_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L45_MS207.2_AB01_Rpb1/2019-08-12-190722L45_MS207.2_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L45_MS207.2_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L46_MS208.2_AB01_Rpb1/2019-08-12-190722L46_MS208.2_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L46_MS208.2_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L47_MS209_AB01_Rpb1/2019-08-12-190722L47_MS209_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L47_MS209_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L48_MS289.2_AB01_Rpb1/2019-08-12-190722L48_MS289.2_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L48_MS289.2_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L49_MS207.1_AB04_Rpb1-S2P/2019-08-12-190722L49_MS207.1_AB04_Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-12-190722L49_MS207.1_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L50_MS208.1_AB04_Rpb1-S2P/2019-08-12-190722L50_MS208.1_AB04_Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-12-190722L50_MS208.1_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L51_MS281_AB04_Rpb1-S2P/2019-08-12-190722L51_MS281_AB04_Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-12-190722L51_MS281_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L52_MS282_AB04_Rpb1-S2P/2019-08-12-190722L52_MS282_AB04_Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-12-190722L52_MS282_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L53_MS283.1_AB04_Rpb1-S2P/2019-08-12-190722L53_MS283.1_AB04_Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-12-190722L53_MS283.1_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L54_MS284_AB04_Rpb1-S2P/2019-08-12-190722L54_MS284_AB04_Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-12-190722L54_MS284_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L55_MS285_AB04_Rpb1-S2P/2019-08-12-190722L55_MS285_AB04_Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-12-190722L55_MS285_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L56_MS289_AB04_Rpb1-S2P/2019-08-12-190722L56_MS289_AB04_Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-12-190722L56_MS289_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L57_MS207.2_AB04_Rpb1-S2P/2019-08-12-190722L57_MS207.2_AB04_Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-12-190722L57_MS207.2_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L58_MS208.2_AB04_Rpb1-S2P/2019-08-12-190722L58_MS208.2_AB04_Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-12-190722L58_MS208.2_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L59_MS209_AB04_Rpb1-S2P/2019-08-12-190722L59_MS209_AB04_Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-12-190722L59_MS209_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L60_MS289.2_AB04_Rpb1-S2P/2019-08-12-190722L60_MS289.2_AB04_Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-12-190722L60_MS289.2_AB04_Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L61_MS207.2_AB01_Rpb1_RA/2019-08-12-190722L61_MS207.2_AB01_Rpb1_RA.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 TSS-250bp-350bp-merged.2019-08-12-190722L61_MS207.2_AB01_Rpb1_RA.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L62_MS207.2_AB01_Rpb1_RB/2019-08-12-190722L62_MS207.2_AB01_Rpb1_RB.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 TSS-250bp-350bp-merged.2019-08-12-190722L62_MS207.2_AB01_Rpb1_RB.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L63_MS289.2_AB01_Rpb1_RA/2019-08-12-190722L63_MS289.2_AB01_Rpb1_RA.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 TSS-250bp-350bp-merged.2019-08-12-190722L63_MS289.2_AB01_Rpb1_RA.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L64_MS28.29_AB01_Rpb1_RB/2019-08-12-190722L64_MS28.29_AB01_Rpb1_RB.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 TSS-250bp-350bp-merged.2019-08-12-190722L64_MS28.29_AB01_Rpb1_RB.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L65_MS521_AB101_GFP-NLS-V5/2019-08-12-190722L65_MS521_AB101_GFP-NLS-V5.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L65_MS521_AB101_GFP-NLS-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L66_MS529_AB101_WHI5-V5/2019-08-12-190722L66_MS529_AB101_WHI5-V5.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L66_MS529_AB101_WHI5-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L67_MS527_AB101_STB1-V5/2019-08-12-190722L67_MS527_AB101_STB1-V5.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L67_MS527_AB101_STB1-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L68_MS522_AB101_SWI4-V5/2019-08-12-190722L68_MS522_AB101_SWI4-V5.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L68_MS522_AB101_SWI4-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L69_MS524_AB101_SWI6-V5/2019-08-12-190722L69_MS524_AB101_SWI6-V5.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L69_MS524_AB101_SWI6-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L70_MS528_AB101_BCK2-V5/2019-08-12-190722L70_MS528_AB101_BCK2-V5.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L70_MS528_AB101_BCK2-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L71_MS523_AB101_MBP1-V5/2019-08-12-190722L71_MS523_AB101_MBP1-V5.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L71_MS523_AB101_MBP1-V5.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-12-190722L72_MS283.1_AB01_Rpb1/2019-08-12-190722L72_MS283.1_AB01_Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-12-190722L72_MS283.1_AB01_Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L17_MS207.1-RAPA_AB1-Rpb1/2019-08-28-MS190729L17_MS207.1-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L17_MS207.1-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L18_MS208.1-RAPA_AB1-Rpb1/2019-08-28-MS190729L18_MS208.1-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L18_MS208.1-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L19_MS281-RAPA_AB1-Rpb1/2019-08-28-MS190729L19_MS281-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L19_MS281-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L20_MS282-RAPA_AB1-Rpb1/2019-08-28-MS190729L20_MS282-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L20_MS282-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L21_MS283.1-RAPA_AB1-Rpb1/2019-08-28-MS190729L21_MS283.1-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L21_MS283.1-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L22_MS284-RAPA_AB1-Rpb1/2019-08-28-MS190729L22_MS284-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L22_MS284-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L23_MS285-RAPA_AB1-Rpb1/2019-08-28-MS190729L23_MS285-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L23_MS285-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L24_MS289.1-RAPA_AB1-Rpb1/2019-08-28-MS190729L24_MS289.1-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L24_MS289.1-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L25_MS207.2-RAPA_AB1-Rpb1/2019-08-28-MS190729L25_MS207.2-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L25_MS207.2-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L26_MS208.2-RAPA_AB1-Rpb1/2019-08-28-MS190729L26_MS208.2-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L26_MS208.2-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L27_MS209-RAPA_AB1-Rpb1/2019-08-28-MS190729L27_MS209-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L27_MS209-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L28_MS283.2-RAPA_AB1-Rpb1/2019-08-28-MS190729L28_MS283.2-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L28_MS283.2-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L29_MS286-RAPA_AB1-Rpb1/2019-08-28-MS190729L29_MS286-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L29_MS286-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L30_MS287-RAPA_AB1-Rpb1/2019-08-28-MS190729L30_MS287-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L30_MS287-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L31_MS288-RAPA_AB1-Rpb1/2019-08-28-MS190729L31_MS288-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L31_MS288-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L32_MS289.2-RAPA_AB1-Rpb1/2019-08-28-MS190729L32_MS289.2-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L32_MS289.2-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L33_MS207-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L33_MS207-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L33_MS207-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L34_MS208-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L34_MS208-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L34_MS208-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L35_MS281-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L35_MS281-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L35_MS281-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L36_MS282-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L36_MS282-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L36_MS282-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L37_MS283-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L37_MS283-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L37_MS283-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L38_MS284-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L38_MS284-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L38_MS284-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L39_MS285-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L39_MS285-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L39_MS285-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L40_MS289-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L40_MS289-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L40_MS289-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L41_MS207.2-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L41_MS207.2-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L41_MS207.2-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L42_MS208.2-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L42_MS208.2-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L42_MS208.2-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L43_MS209-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L43_MS209-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L43_MS209-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L44_MS283.2-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L44_MS283.2-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L44_MS283.2-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L45_MS286-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L45_MS286-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L45_MS286-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L46_MS287-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L46_MS287-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L46_MS287-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L47_MS288-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L47_MS288-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L47_MS288-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L48_MS289.2-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L48_MS289.2-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L48_MS289.2-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L49_MS207-RAPA_AB1-Rpb1/2019-08-28-MS190729L49_MS207-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L49_MS207-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L50_MS208-RAPA_AB1-Rpb1/2019-08-28-MS190729L50_MS208-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L50_MS208-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L51_MS282-RAPA_AB1-Rpb1/2019-08-28-MS190729L51_MS282-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L51_MS282-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L52_MS207.2-RAPA_AB1-Rpb1/2019-08-28-MS190729L52_MS207.2-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L52_MS207.2-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L53_MS208.2-RAPA_AB1-Rpb1/2019-08-28-MS190729L53_MS208.2-RAPA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L53_MS208.2-RAPA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L54_MS207-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L54_MS207-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L54_MS207-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L55_MS208-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L55_MS208-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L55_MS208-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L56_MS283-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L56_MS283-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L56_MS283-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L58_MS208.2-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L58_MS208.2-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L58_MS208.2-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L59_MS287-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L59_MS287-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L59_MS287-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190729L60_MS288-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190729L60_MS288-RAPA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190729L60_MS288-RAPA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L01_MS55_FrA_input/2019-08-28-MS190807L01_MS55_FrA_input.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L01_MS55_FrA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L02_MS55_FrB_input/2019-08-28-MS190807L02_MS55_FrB_input.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L02_MS55_FrB_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L03_MS55_FrC_input/2019-08-28-MS190807L03_MS55_FrC_input.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L03_MS55_FrC_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L04_MS55_FrD_input/2019-08-28-MS190807L04_MS55_FrD_input.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L04_MS55_FrD_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L05_MS55_FrE_input/2019-08-28-MS190807L05_MS55_FrE_input.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L05_MS55_FrE_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L06_MS55_FrF_input/2019-08-28-MS190807L06_MS55_FrF_input.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L06_MS55_FrF_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L07_MS55_FrA_AB1-Rpb1/2019-08-28-MS190807L07_MS55_FrA_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L07_MS55_FrA_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L08_MS55_FrB_AB1-Rpb1/2019-08-28-MS190807L08_MS55_FrB_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L08_MS55_FrB_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L09_MS55_FrC_AB1-Rpb1/2019-08-28-MS190807L09_MS55_FrC_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L09_MS55_FrC_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L10_MS55_FrD_AB1-Rpb1/2019-08-28-MS190807L10_MS55_FrD_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L10_MS55_FrD_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L11_MS55_FrE_AB1-Rpb1/2019-08-28-MS190807L11_MS55_FrE_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L11_MS55_FrE_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L12_MS55_FrF_AB1-Rpb1/2019-08-28-MS190807L12_MS55_FrF_AB1-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L12_MS55_FrF_AB1-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L13_MS55_FrA_AB4-Rpb1-S2P/2019-08-28-MS190807L13_MS55_FrA_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L13_MS55_FrA_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L14_MS55_FrB_AB4-Rpb1-S2P/2019-08-28-MS190807L14_MS55_FrB_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L14_MS55_FrB_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L15_MS55_FrC_AB4-Rpb1-S2P/2019-08-28-MS190807L15_MS55_FrC_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L15_MS55_FrC_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L16_MS55_FrD_AB4-Rpb1-S2P/2019-08-28-MS190807L16_MS55_FrD_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L16_MS55_FrD_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L17_MS55_FrE_AB4-Rpb1-S2P/2019-08-28-MS190807L17_MS55_FrE_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L17_MS55_FrE_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L18_MS55_FrF_AB4-Rpb1-S2P/2019-08-28-MS190807L18_MS55_FrF_AB4-Rpb1-S2P.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L18_MS55_FrF_AB4-Rpb1-S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L50_MS55_FrC_input_R/2019-08-28-MS190807L50_MS55_FrC_input_R.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L50_MS55_FrC_input_R.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L51_MS55_FrE_input_R/2019-08-28-MS190807L51_MS55_FrE_input_R.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L51_MS55_FrE_input_R.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L52_MS55_FrF_input_R/2019-08-28-MS190807L52_MS55_FrF_input_R.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 TSS-250bp-350bp-merged.2019-08-28-MS190807L52_MS55_FrF_input_R.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L01_MS55_A_input/2019-10-07-190923L01_MS55_A_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L01_MS55_A_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L02_MS55_B_input/2019-10-07-190923L02_MS55_B_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L02_MS55_B_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L03_MS55_C_input/2019-10-07-190923L03_MS55_C_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L03_MS55_C_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L04_MS55_D_input/2019-10-07-190923L04_MS55_D_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L04_MS55_D_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L05_MS55_E_input/2019-10-07-190923L05_MS55_E_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L05_MS55_E_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L06_MS55_F_input/2019-10-07-190923L06_MS55_F_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L06_MS55_F_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L07_MS55_A_AB01-Rpb1/2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L07_MS55_A_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L08_MS55_B_AB01-Rpb1/2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L08_MS55_B_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L09_MS55_C_AB01-Rpb1/2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L09_MS55_C_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L10_MS55_D_AB01-Rpb1/2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L10_MS55_D_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L11_MS55_E_AB01-Rpb1/2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L11_MS55_E_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L12_MS55_F_AB01-Rpb1/2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L12_MS55_F_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P/2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.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 TSS-250bp-350bp-merged.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P/2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.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 TSS-250bp-350bp-merged.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P/2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.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 TSS-250bp-350bp-merged.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P/2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.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 TSS-250bp-350bp-merged.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P/2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.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 TSS-250bp-350bp-merged.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P/2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.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 TSS-250bp-350bp-merged.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L19_MS55_A_AB20-H3/2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L19_MS55_A_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L20_MS55_B_AB20-H3/2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L20_MS55_B_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L21_MS55_C_AB20-H3/2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L21_MS55_C_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L22_MS55_D_AB20-H3/2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L22_MS55_D_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L23_MS55_E_AB20-H3/2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L23_MS55_E_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L24_MS55_F_AB20-H3/2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L24_MS55_F_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L25_MS55_A_AB21-H4/2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L25_MS55_A_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L26_MS55_B_AB21-H4/2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L26_MS55_B_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L27_MS55_C_AB21-H4/2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L27_MS55_C_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L28_MS55_D_AB21-H4/2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L28_MS55_D_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L29_MS55_E_AB21-H4/2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L29_MS55_E_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L30_MS55_F_AB21-H4/2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L30_MS55_F_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L31_MS55_A_AB48-H3K36me3/2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L32_MS55_B_AB48-H3K36me3/2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L33_MS55_C_AB48-H3K36me3/2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L34_MS55_D_AB48-H3K36me3/2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L35_MS55_E_AB48-H3K36me3/2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L36_MS55_F_AB48-H3K36me3/2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L55_MS283.2_input/2019-10-07-190923L55_MS283.2_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L55_MS283.2_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L56_MS286_input/2019-10-07-190923L56_MS286_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L56_MS286_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L57_MS287_input/2019-10-07-190923L57_MS287_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L57_MS287_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L58_MS288_input/2019-10-07-190923L58_MS288_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L58_MS288_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L59_MS88_FrA_input/2019-10-07-190923L59_MS88_FrA_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L59_MS88_FrA_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L60_MS88_FrB_input/2019-10-07-190923L60_MS88_FrB_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L60_MS88_FrB_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L61_MS88_FrC_input/2019-10-07-190923L61_MS88_FrC_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L61_MS88_FrC_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L62_MS88_FrD_input/2019-10-07-190923L62_MS88_FrD_input.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 TSS-250bp-350bp-merged.2019-10-07-190923L62_MS88_FrD_input.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L63_MS88_FrA_AB01-Rpb1/2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L64_MS88_FrB_AB01-Rpb1/2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L65_MS88_FrC_AB01-Rpb1/2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L66_MS88_FrD_AB01-Rpb1/2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P/2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.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 TSS-250bp-350bp-merged.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P/2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.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 TSS-250bp-350bp-merged.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P/2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.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 TSS-250bp-350bp-merged.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P/2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.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 TSS-250bp-350bp-merged.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L71_MS88_FrA_AB20-H3/2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L71_MS88_FrA_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L72_MS88_FrB_AB20-H3/2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L72_MS88_FrB_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L73_MS88_FrC_AB20-H3/2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L73_MS88_FrC_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L74_MS88_FrD_AB20-H3/2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L74_MS88_FrD_AB20-H3.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L75_MS88_FrA_AB21-H4/2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L75_MS88_FrA_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L76_MS88_FrB_AB21-H4/2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L76_MS88_FrB_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L77_MS88_FrC_AB21-H4/2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L77_MS88_FrC_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L78_MS88_FrD_AB21-H4/2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.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 TSS-250bp-350bp-merged.2019-10-07-190923L78_MS88_FrD_AB21-H4.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R/2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.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 TSS-250bp-350bp-merged.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.a.ERMTOC.RPM -RPM -excludeReadsMappingToOtherChromosomes