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Welcome to the Evolution of DNA methylation project

This is a research repo for our project, entitled "Evolutionary and functional genomics of DNA methylation in maize domestication and improvement".

Introduction

In this study, we leveraged whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) on populations of modern maize, landrace, and teosinte Zea mays ssp. parviglumis to investigate the adaptive and phenotypic consequences of methylation variation in maize.

Architecture about this Repo

This project contains ~540 commits. A largedata directory was intentionally ignored by adding to gitignore because of the large size of the files within the folder. To guide the visitors having a better idea about the repo, here we briefly introduce the functions or sepecific purposes of the directory system. The layout of directories is based on the idea from ProjectTemplate.

  1. cache: Here we store intermediate data sets that are generated during a preprocessing step.
  2. data: Here we store our raw data of small size. Data of large size, i.e. > 100M, store in a largedata folder that has been ignored using gitignore.
  3. reports: Documentation codes (i.e. Rmd files) for generating the figures.
  4. graphs: Graphs produced during the study.
  5. lib: Some functions for our work.
  6. profilling: Analysis scripts for the project. It contains some sub-directories.
  7. table: Table produced during the study.

Figures:

Rmd code to generate Figures in the paper.

  1. Figure 1: Panels of this figure can be produced with code reports/Fig1_sfs.Rmd. And the Figure1 in a pdf version.
  2. Figure 2: Panels of this figure can be produced with code reports/Fig2_Circos_Plot.Rmd. And the Figure2 in a pdf version.
  3. Figure 3: Panels of this figure can be produced with code reports/Fig3_CG_DMR_Function.Rmd. And the Figure3 in a pdf version.
  4. Figure 4: Panels of this figure can be produced with code reports/Fig4_VCAP_Vgt1.Rmd. And the Figure4 in a pdf version.
  5. Figure 5: Panels of this figure can be produced with code reports/Fig5_tb1.Rmd. And the Figure5 in a pdf version.

Supplementary Tables:

License

This repo is free and open source for research usage, licensed under GPLv2.

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mSFS using a teosinte natural population

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