ChromHMM Report

Input Directory: /net/isilon5/encode/work/akundaje/work/liz/segmentation/binaryTracks/combrep
Output Directory: /net/isilon5/encode/work/akundaje/work/liz/segmentation/results/S14
Number of States: 14
Assembly: mm9
Full ChromHMM command: LearnModel -b 200 -f /net/isilon5/encode/work/akundaje/work/liz/segmentation/binaryTracks/combrep/filelist.tab -i mm9neurodegen -l /net/isilon5/encode/work/akundaje/work/encode/rawdata/annotations/genomeSize/mm9.genome /net/isilon5/encode/work/akundaje/work/liz/segmentation/binaryTracks/combrep /net/isilon5/encode/work/akundaje/work/liz/segmentation/results/S14 14 mm9

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

  • control-2wk_14_mm9neurodegen Segmentation File (Four Column Bed File)
  • control-6wk_14_mm9neurodegen Segmentation File (Four Column Bed File)
  • treat-2wk_14_mm9neurodegen Segmentation File (Four Column Bed File)
  • treat-6wk_14_mm9neurodegen Segmentation File (Four Column Bed File)

    Custom Tracks for loading into the UCSC Genome Browser:
  • control-2wk_14_mm9neurodegen Browser Custom Track Dense File
  • control-2wk_14_mm9neurodegen Browser Custom Track Expanded File
  • control-6wk_14_mm9neurodegen Browser Custom Track Dense File
  • control-6wk_14_mm9neurodegen Browser Custom Track Expanded File
  • treat-2wk_14_mm9neurodegen Browser Custom Track Dense File
  • treat-2wk_14_mm9neurodegen Browser Custom Track Expanded File
  • treat-6wk_14_mm9neurodegen Browser Custom Track Dense File
  • treat-6wk_14_mm9neurodegen Browser Custom Track Expanded File

    State Enrichments

    control-2wk_14_mm9neurodegen Enrichments


  • control-2wk_14_mm9neurodegen Overlap Enrichment SVG File
  • control-2wk_14_mm9neurodegen Overlap Enrichment Tab-Delimited Text File

  • control-2wk_14_mm9neurodegen_RefSeqTES_neighborhood Enrichment SVG File
  • control-2wk_14_mm9neurodegen_RefSeqTES_neighborhood Enrichment Tab-Delimited Text File

  • control-2wk_14_mm9neurodegen_RefSeqTSS_neighborhood Enrichment SVG File
  • control-2wk_14_mm9neurodegen_RefSeqTSS_neighborhood Enrichment Tab-Delimited Text File

    control-6wk_14_mm9neurodegen Enrichments


  • control-6wk_14_mm9neurodegen Overlap Enrichment SVG File
  • control-6wk_14_mm9neurodegen Overlap Enrichment Tab-Delimited Text File

  • control-6wk_14_mm9neurodegen_RefSeqTES_neighborhood Enrichment SVG File
  • control-6wk_14_mm9neurodegen_RefSeqTES_neighborhood Enrichment Tab-Delimited Text File

  • control-6wk_14_mm9neurodegen_RefSeqTSS_neighborhood Enrichment SVG File
  • control-6wk_14_mm9neurodegen_RefSeqTSS_neighborhood Enrichment Tab-Delimited Text File

    treat-2wk_14_mm9neurodegen Enrichments


  • treat-2wk_14_mm9neurodegen Overlap Enrichment SVG File
  • treat-2wk_14_mm9neurodegen Overlap Enrichment Tab-Delimited Text File

  • treat-2wk_14_mm9neurodegen_RefSeqTES_neighborhood Enrichment SVG File
  • treat-2wk_14_mm9neurodegen_RefSeqTES_neighborhood Enrichment Tab-Delimited Text File

  • treat-2wk_14_mm9neurodegen_RefSeqTSS_neighborhood Enrichment SVG File
  • treat-2wk_14_mm9neurodegen_RefSeqTSS_neighborhood Enrichment Tab-Delimited Text File

    treat-6wk_14_mm9neurodegen Enrichments


  • treat-6wk_14_mm9neurodegen Overlap Enrichment SVG File
  • treat-6wk_14_mm9neurodegen Overlap Enrichment Tab-Delimited Text File

  • treat-6wk_14_mm9neurodegen_RefSeqTES_neighborhood Enrichment SVG File
  • treat-6wk_14_mm9neurodegen_RefSeqTES_neighborhood Enrichment Tab-Delimited Text File

  • treat-6wk_14_mm9neurodegen_RefSeqTSS_neighborhood Enrichment SVG File
  • treat-6wk_14_mm9neurodegen_RefSeqTSS_neighborhood Enrichment Tab-Delimited Text File