2020.11.11丨三代细菌甲基化流程调研

• pipeline
  • Figure
    • pipeline
      • Figure
        • http://blog.sina.com.cn/s/blog_12b14648e0102vetw.html
        • 
        • http://www.biomarker.com.cn/technology-services/medicine-ont-methylation
        • 
      • step.1 quality control
        • fastQC
      • step.2 trim
        • trim-galore
        • Trimmomatic 
      • step.3 Align to the genome
        • ONT:minimap2
          • https://github.com/lh3/minimap2
          • https://mp.weixin.qq.com/s?__biz=MzI2MjA1MDQxMg==&mid=2649709957&idx=1&sn=fde0cc6a08ca0f9fcdc6ca6c6e281226&chksm=f24afa86c53d73902d3a81c66c9d5c3292c35e399cdee9935bf10896fc1164afeb212ce8c7c4&scene=21#wechat_redirect
        • PB:bismark
        • SNP: MAUVE 2.3.1
      • step.4 Basecalling
        • guppy
          • https://zhuanlan.zhihu.com/p/91629796
        • nanopolish
          • https://blog.youkuaiyun.com/weixin_41869644/article/details/89083405
          • https://blog.youkuaiyun.com/weixin_41869644/article/details/88956794
      • step.5 identification of modifi
        • ONT：Tombo
          • https://github.com/nanoporetech/tombo
          • https://blog.youkuaiyun.com/weixin_41869644/article/details/90230535
          • https://mp.weixin.qq.com/s?__biz=MzI2MjA1MDQxMg==&mid=2649710160&idx=1&sn=8307f6ada2380fd22bccae3d6c424341&chksm=f24af953c53d7045e202e987fdf5dc0bc820a8ed5cdc76ff9f74bbf5aa0ff68a0fa3d0129c54&scene=21#wechat_redirect
        • PB：
          • MEME-ChIP、 REBASE
            • Machanick,P. and Bailey,T.L. (2011) MEME-ChIP: motif analysis oflarge DNA datasets. Bioinformatics, 27, 1696–1697.
            • Roberts,R.J., Vincze,T., Posfai,J. and Macelis,D. (2015) REBASE––adatabase for DNA restriction and modification: enzymes, genes andgenomes. Nucleic Acids Res., 43, D298–D299.
          • SMRT Portal
            • standard settings
              • ‘Motif score’ = (number of detections matching motif) / (number of genomesites matching motif) × (sum of log-p value of detectionsmatching motif) = (fraction methylated) × (sum of log-pvalues of matches). SMRT Portal searches (close to maximize) through the space of all possible motifs, progressivelytesting longer motifs using a branch-and-bound search. Theminimal term ‘motif score’ is 40 and ‘fraction methylated’term must be less than 1.
        • MEGA
        • ClustalW
      • step.6 DMR analysis
        • R package
          • methylKit
          • eDMR
          • others
            • table 1
            • table 2
        • annotation：iTOL
      • step.7 enrichment analysis
        • GO
        • KEGG
      • step.8 relate sample analysis
        • eDMR
      • Multi-functional software
        • Multi-functional software
    • result
      • Raw data/Clean data
      • mapping
      • base calling
      • MOTIF、logo
      • PCA
      • circle
      • annotate
      • GO、KEGG enrichment analysis
    •