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methylkit：用于高通量亚硫酸氢盐测序的DNA甲基化分析和注释的R包。该包的目的是处理RRBS以及WGBS的测序数据。此外，也可以处理从Tab-seq或oxBS-seq获得的5hmC的碱基对分辨率数据。

DSS：该软件包专为高通量测序数据的差异分析而设计，依赖于bsseq包。它提供了用于分析RNA-seq 差异表达和亚硫酸氢盐测序 (BS-seq) 差异甲基化的功能。DSS 的核心是一个基于分层贝叶斯模型的程序，用于估计和缩小基因或 CpG 位点特异性分散，然后进行 Wald 检验以检测差异表达/甲基化。

dmrseq：这个包建立在bsseq包的基础上，bsseq包提供了亚硫酸氢盐测序数据的有效存储和操作以及对差异甲基化cpg的推断。dmrseq的主要目的是检测差异甲基化区域或CpGs。

使用methylKit分析过程如下：

1、/TJPROJ6/RNA_SH/personal_dir/zhangxin/jiaoben/jiajihua/diff_DMR/methylKit/Diff_dmr_prepare.py  #拆分cx report数据
usage: Diff_dmr_prepare.py [opthions] [value]

This program is used to prepare methylKit or DSS infile

optional arguments:
  -h, --help            show this help message and exit
  -CX , --cx_repot      the cx report file
  -F , --fai            the fai file
  -N SPLIT_NUMBER, --split_number SPLIT_NUMBER
                      the cx repot split number, default:20
  -MD MIN_DEPTH, --min_depth MIN_DEPTH
                      the min reads depth for C site, default:4
  -MMC MIN_MC, --min_mC MIN_MC
                      the min mC reads depth for C site, default:1
  -OF {DSS,methylKit}, --outformate {DSS,methylKit}
                      the out file formate, DSS prepare suggest to use
                      script in pipline
  -S , --sample         the sample name
  -O , --out            the out dir
2、/TJPROJ6/RNA_SH/personal_dir/zhangxin/jiaoben/jiajihua/diff_DMR/methylKit/product_diff.py  #生成差异分析脚本
  optional arguments:
  -h, --help            show this help message and exit
  -SD SPLIT_CX_DIR, --split_cx_dir SPLIT_CX_DIR
                      the split cx file dir
  -C CONDITION, --condition CONDITION
                      the condition file
  -CP COMPARE, --compare COMPARE
                      the compare
  -D DIFFERENCE, --difference DIFFERENCE
                      the difference , default:25
  -PJ PADJ, --padj PADJ
                      the padj , default:0.05
  -PV PVALUE, --pvalue PVALUE
                      the pvalue
  -A ANALYSIS, --analysis ANALYSIS
                      dml or dmr, default:dmr
  -O OUTDIR, --outdir OUTDIR
                      the out dir

                      

DMC的脚本使用：/TJPROJ6/RNA_SH/personal_dir/fengjie/Personal_analysis/methylKit/methylKit.R

                   
                   
3、/TJPROJ6/RNA_SH/personal_dir/zhangxin/jiaoben/jiajihua/diff_DMR/methylKit/merge_methylKit.py  #合并拆分分析结果
This program is used to merge methylKit result

optional arguments:
  -h, --help            show this help message and exit
  -I INDIR, --indir INDIR
                      the methylKit.R analysis out dir
  -O OUT, --out OUT     the outdir
 示例：
  python /TJPROJ6/RNA_SH/personal_dir/zhangxin/jiaoben/jiajihua/diff_DMR/methylKit/merge_methylKit.py --indir /TJPROJ12/RNA_SH/shouhou/202410/X101SC24062171-Z01-J006_methylkit/DMC/WT1vsCK1 --out /TJPROJ12/RNA_SH/shouhou/202410/X101SC24062171-Z01-J006_methylkit/DMC/WT1vsCK1

4、合并三个序列环境并转换成DSS格式：

/TJPROJ6/RNA_SH/personal_dir/zhangxin/jiaoben/jiajihua/diff_DMR/methylKit/methylKit_to_DSS.py
python /TJPROJ6/RNA_SH/personal_dir/zhangxin/jiaoben/jiajihua/diff_DMR/methylKit/methylKit_to_DSS.py WT1vsCK1_cg_DM_all.xls,WT1vsCK1_chg_DM_all.xls,WT1vsCK1_chh_DM_all.xls WT1vsCK1_DM_all.xls /TJPROJ12/RNA_SH/shouhou/202410/X101SC24062171-Z01-J006_methylkit/condition.xls WT1vsCK1