faith-hplc / m6a_evolution

A bioinformatics pipeline for the evolution analysis of m6A in plants

m6A_Evolution

A bioinformatics pipeline for the evolution analysis of m⁶A in plants (Miao et al. Molecular Biology and Evolution)

Graphic illustration of the evolutionary implications of m⁶A methylome in plants

Directory structure

├── Part_1/
│   ├── ready_to_get_m6A_genes.R
│   ├── data1_m6A_peaks_genes.RData.gz
│   ├── ready_to_gene_attributes.R
│   ├── data2_gene_attributes.RData.gz
│   ├── sample_correlations.R
│   ├── part1_plots_m6A_ratios.R
│   ├── GO_enrichment.R
│   ├── figures
│   └── workflow/
│       ├── gene_list/: expressed genes and m6A genes
│       ├── m6Apipeline.sh: peak calling for strand-specific m6A-Seq data
│       ├── scripts/
│       │   ├── PEA_peak_calling.R
│       │   ├── diffbind2.R
│       │   ├── read_distribution_using_trumpet.R
│       │   ├── samples_gene_merge.R
│       │   ├── samples_peak_merge.R
│       │   ├── split.sh
│       │   └── split_c.sh
│       └── snakemake/: pipelines for public data
├── Part_2
│   ├── part2_plots_evolutionary_origins.R
│   └── figures
├── Part_3
│   ├── part3_plots_evolutionary_constraints.R
│   ├── KaKs_m6A_divergence.sh
│   └── figures
├── Part_4
│   ├── part4_plots_subgenome_divergence.R
│   └── figures
├── Part_5
│   ├── part5_plots_gene_expansions.R
│   └── figures
├── Part_6
│   ├── part6_plot_m6A_translation.R
│   └── figures
└── figure7.png

How to access help

• For any feedback and suggestions, please feel free to leave a message at Github issues. We will try our best to deal with all issues as soon as possible.
• In addition, if any suggestions are available, feel free to contact: Ting Zhang [email protected] or Chuang Ma [email protected]

Citation

Zhenyan Miao, Ting Zhang, Bin Xie, Yuhong Qi, Chuang Ma, Evolutionary implications of the RNA N6-methyladenosine methylome in plants, Molecular Biology and Evolution, 2021, msab299, https://doi.org/10.1093/molbev/msab299