<rnb.xml>
<analysis.name>BLUEPRINT WGBS - bpRel201609_rnb_v02</analysis.name>
<assembly>hg38</assembly>
<data.type>bed.dir</data.type>
<import.table.separator>\t</import.table.separator>
<import.bed.style>EPP</import.bed.style>
<analyze.sites>false</analyze.sites>
<region.types>tiling,cpgislands,genes,promoters,tiling1kb,gencode22promoters,ensembleRegBuildBPall</region.types>
<identifiers.column>sampleName</identifiers.column>
<colors.category>#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666,#2166AC,#B2182B,#00441B,#40004B,#053061,#003D7C,#D50911</colors.category>
<colors.meth>#EDF8B1,#41B6C4,#081D58</colors.meth>
<min.group.size>1</min.group.size>
<max.group.count>15</max.group.count>
<qc.coverage.plots>false</qc.coverage.plots>
<qc.coverage.histograms>false</qc.coverage.histograms>
<qc.coverage.violins>false</qc.coverage.violins>
<qc.coverage.threshold.plot null="null"></qc.coverage.threshold.plot>
<filtering.missing.value.quantile>0.75</filtering.missing.value.quantile>
<filtering.coverage.threshold>5</filtering.coverage.threshold>
<filtering.snp>no</filtering.snp>
<filtering.low.coverage.masking>true</filtering.low.coverage.masking>
<filtering.high.coverage.outliers>true</filtering.high.coverage.outliers>
<filtering.greedycut>false</filtering.greedycut>
<filtering.sex.chromosomes.removal>true</filtering.sex.chromosomes.removal>
<exploratory.columns>cellTypeGroup,tissueTypeShort,DONOR_SEX</exploratory.columns>
<exploratory.intersample>false</exploratory.intersample>
<exploratory.clustering.heatmaps.pdf>true</exploratory.clustering.heatmaps.pdf>
<exploratory.region.profiles></exploratory.region.profiles>
<differential.comparison.columns>cmp_ct_mono_vs_neut,cmp_ct_mono_vs_neut_VB,cmp_ct_mono_vs_mf,cmp_ct_mono_vs_mf_VB,cmp_ct_TCD4_TN_vs_CM,cmp_ct_TCD4_TN_vs_EM,cmp_ct_TCD4_CM_vs_EM,cmp_ct_TCD8_TN_vs_CM,cmp_ct_TCD8_TN_vs_EM,cmp_ct_TCD8_CM_vs_EM,cmp_ct_neut_myel_vs_meta,cmp_ct_neut_meta_vs_band,cmp_ct_neut_band_vs_segm,cmp_ct_neut_early_vs_mature</differential.comparison.columns>
<covariate.adjustment.columns>tissueTypeShort,DONOR_SEX</covariate.adjustment.columns>
<differential.enrichment>true</differential.enrichment>
<differential.report.sites>false</differential.report.sites>
<replicate.id.column null="null"></replicate.id.column>
<export.to.trackhub>bigBed</export.to.trackhub>
<export.types>tiling,tiling1kb,ensembleRegBuildBPall,gencode22promoters</export.types>
<logging.memory>true</logging.memory>
<logging.disk>true</logging.disk>
<disk.dump.big.matrices>true</disk.dump.big.matrices>
<disk.dump.bigff>true</disk.dump.bigff>
<disk.dump.bigff.finalizer>delete</disk.dump.bigff.finalizer>
<enforce.memory.management>true</enforce.memory.management>
<gz.large.files>true</gz.large.files>
<import.skip.object.check>true</import.skip.object.check>
</rnb.xml>
