DNA Methylation Sequencing Analysis
  • Introduction
  • Data Preparation
    • Locate the MethPipe Files
    • Download Utilities
    • Download Annotations
    • Annotation File Preparation – Defining Genomic Regions
  • Analysis Work Flow
    • DNA Methylation at Genomic Bins
    • DNA Methylation at CpG Islands
    • DNA Methylation at TFBS
    • DNA Methylation at Various Genic Structure Regions
    • DNA Methylation at Repeat Elements
    • Add CpG Islands Co-localization Information to HMR BED Files
    • Similarity and Differences of HMRs and PMDs from H1 and IMR90
      • HMRs
      • PMDs
  • Visualization Using R
    • Install R Libraries
    • Execute the R Scripts
  • An introduction of UCSC Genome Browser
    • General Usage
    • The Compressed Binary Index Format
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Analysis Work Flow

In this section, we will show readers how to use the intersectbed program of the bedtools utilities to identify the overlapped features in two sets of genomic features. Additionally, the groupBy program is then used to summarized statistics on selected data column(s) based upon common column groupings.

In DNA methylation analysis, this may be the mean methylation levels of promoter regions, whether the HMRs identified between two cells lines co-occur or are specific to each cell lines, or divide the HMRs into CpG island-containing and without CpG island.

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Last updated 5 years ago

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