> For the complete documentation index, see [llms.txt](https://ycl6.gitbook.io/methylation-sequencing-analysis/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://ycl6.gitbook.io/methylation-sequencing-analysis/analysis_work_flow.md).

# 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.