ChromHMM Report

Input Directory: /projects/mbilenky/CEMT/breast/forChromHMM/
Output Directory: /projects/production_genomics/CEMT/breast/finder/chromhmm_18_state_Misha_binned/
Number of States: 18
Assembly: hg19
Full ChromHMM command: LearnModel -b 200 -p 6 /projects/mbilenky/CEMT/breast/forChromHMM/ /projects/production_genomics/CEMT/breast/finder/chromhmm_18_state_Misha_binned/ 18 hg19

Model Parameters


  • Emission Parameter SVG File
  • Emission Parameter Tab-Delimited Text File

  • Transition Parameter SVG File
  • Transition Parameter Tab-Delimited Text File

  • All Model Parameters Tab-Delimited Text File

    Genome Segmentation Files

  • CEMT_35_18 Segmentation File (Four Column Bed File)
  • CEMT_36_18 Segmentation File (Four Column Bed File)
  • CEMT_37_18 Segmentation File (Four Column Bed File)
  • CEMT_38_18 Segmentation File (Four Column Bed File)

    Custom Tracks for loading into the UCSC Genome Browser:
  • CEMT_35_18 Browser Custom Track Dense File
  • CEMT_35_18 Browser Custom Track Expanded File
  • CEMT_36_18 Browser Custom Track Dense File
  • CEMT_36_18 Browser Custom Track Expanded File
  • CEMT_37_18 Browser Custom Track Dense File
  • CEMT_37_18 Browser Custom Track Expanded File
  • CEMT_38_18 Browser Custom Track Dense File
  • CEMT_38_18 Browser Custom Track Expanded File

    State Enrichments

    CEMT_35_18 Enrichments


  • CEMT_35_18 Overlap Enrichment SVG File
  • CEMT_35_18 Overlap Enrichment Tab-Delimited Text File

  • CEMT_35_18_RefSeqTES_neighborhood Enrichment SVG File
  • CEMT_35_18_RefSeqTES_neighborhood Enrichment Tab-Delimited Text File

  • CEMT_35_18_RefSeqTSS_neighborhood Enrichment SVG File
  • CEMT_35_18_RefSeqTSS_neighborhood Enrichment Tab-Delimited Text File

    CEMT_36_18 Enrichments


  • CEMT_36_18 Overlap Enrichment SVG File
  • CEMT_36_18 Overlap Enrichment Tab-Delimited Text File

  • CEMT_36_18_RefSeqTES_neighborhood Enrichment SVG File
  • CEMT_36_18_RefSeqTES_neighborhood Enrichment Tab-Delimited Text File

  • CEMT_36_18_RefSeqTSS_neighborhood Enrichment SVG File
  • CEMT_36_18_RefSeqTSS_neighborhood Enrichment Tab-Delimited Text File

    CEMT_37_18 Enrichments


  • CEMT_37_18 Overlap Enrichment SVG File
  • CEMT_37_18 Overlap Enrichment Tab-Delimited Text File

  • CEMT_37_18_RefSeqTES_neighborhood Enrichment SVG File
  • CEMT_37_18_RefSeqTES_neighborhood Enrichment Tab-Delimited Text File

  • CEMT_37_18_RefSeqTSS_neighborhood Enrichment SVG File
  • CEMT_37_18_RefSeqTSS_neighborhood Enrichment Tab-Delimited Text File

    CEMT_38_18 Enrichments


  • CEMT_38_18 Overlap Enrichment SVG File
  • CEMT_38_18 Overlap Enrichment Tab-Delimited Text File

  • CEMT_38_18_RefSeqTES_neighborhood Enrichment SVG File
  • CEMT_38_18_RefSeqTES_neighborhood Enrichment Tab-Delimited Text File

  • CEMT_38_18_RefSeqTSS_neighborhood Enrichment SVG File
  • CEMT_38_18_RefSeqTSS_neighborhood Enrichment Tab-Delimited Text File