python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.0.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.100.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.101.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.102.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.103.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.104.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.105.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.106.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.107.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.108.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.109.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.10.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.110.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.111.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.112.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.113.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.114.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.115.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.116.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.117.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.118.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.119.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.11.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.120.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.121.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.122.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.123.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.124.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.125.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.126.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.127.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.128.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.129.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.12.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.130.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.131.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.132.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.133.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.134.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.135.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.136.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.137.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.138.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.139.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.13.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.140.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.141.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.142.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.143.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.144.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.145.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.146.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.147.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.148.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.149.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.14.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.150.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.151.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.152.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.153.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.154.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.155.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.156.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.157.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.158.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.159.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.15.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.160.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.161.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.162.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.163.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.164.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.165.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.166.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.167.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.168.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.169.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.16.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.170.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.171.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.172.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.173.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.174.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.175.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.176.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.177.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.178.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.179.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.17.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.180.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.181.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.182.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.183.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.184.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.185.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.186.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.187.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.188.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.189.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.18.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.190.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.191.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.192.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.193.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.194.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.195.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.196.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.197.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.198.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.199.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.19.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.1.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.200.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.201.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.202.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.203.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.204.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.205.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.206.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.207.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.208.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.209.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.20.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.210.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.211.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.212.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.213.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.214.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.215.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.216.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.217.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.218.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.219.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.21.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.220.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.221.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.222.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.223.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.224.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.225.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.226.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.227.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.228.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.229.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.22.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.230.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.231.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.232.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.233.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.234.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.235.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.236.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.237.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.238.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.239.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.23.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.240.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.241.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.242.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.243.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.244.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.245.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.246.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.247.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.248.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.249.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.24.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.250.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.251.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.252.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.253.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.254.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.255.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.256.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.257.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.258.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.259.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.25.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.260.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.261.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.262.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.263.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.264.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.265.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.266.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.267.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.268.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.269.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.26.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.270.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.271.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.272.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.273.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.274.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.275.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.276.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.277.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.278.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.279.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.27.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.280.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.281.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.282.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.283.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.284.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.285.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.286.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.287.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.288.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.289.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.28.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.290.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.291.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.292.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.293.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.294.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.295.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.296.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.297.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.298.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.299.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.29.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.2.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.300.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.301.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.302.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.303.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.304.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.305.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.306.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.307.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.308.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.309.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.30.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.310.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.311.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.312.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.313.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.314.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.315.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.316.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.317.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.318.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.319.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.31.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.320.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.321.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.322.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.323.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.324.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.325.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.326.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.327.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.328.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.329.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.32.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.330.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.331.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.332.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.333.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.334.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.335.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.336.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.337.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.33.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.34.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.35.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.36.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.37.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.38.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.39.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.3.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.40.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.41.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.42.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.43.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.44.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.45.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.46.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.47.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.48.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.49.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.4.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.50.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.51.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.52.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.53.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.54.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.55.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.56.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.57.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.58.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.59.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.5.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.60.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.61.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.62.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.63.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.64.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.65.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.66.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.67.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.68.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.69.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.6.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.70.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.71.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.72.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.73.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.74.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.75.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.76.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.77.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.78.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.79.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.7.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.80.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.81.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.82.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.83.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.84.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.85.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.86.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.87.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.88.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.89.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.8.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.90.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.91.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.92.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.93.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.94.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.95.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.96.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.97.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.98.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.99.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only-CG-excluded-1bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only-CG-excluded-1bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only-CG-excluded-1bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only-CG-excluded-2bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only-CG-excluded-2bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only-CG-excluded-2bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only-CG-excluded-3bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only-CG-excluded-3bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only-CG-excluded-3bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only-CG-excluded-4bp.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only-CG-excluded-4bp.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only-CG-excluded-4bp.reads.BI_w10_a10_b10.reads.tsv
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/methylation-reads-tsv-to_coverage.py 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only.reads.tsv 0.5 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only.reads.min_p_val0.4.cutoff_0.5.coverage.BI_w10_a10_b10 -minAbsPValue 0.4 -BayesianIntegration 10 1 10 10 50 -saveNewSingleMoleculeFile 2019_05_29_GM12878_SMAC_SDS_HC.9.tombo.m6A-only.reads.BI_w10_a10_b10.reads.tsv