===== 测试 =====

流程脚本路径：
  /TJPROJ6/NC_BG_SH/personal_dir/liuying/WGBS/Methylation_Pipeline_V7.3.2.qsubname.py
  
测试路径：
  /TJPROJ6/RNA_SH/personal_dir/yangdan/test/DML

**[[流程修改日志]]**
----

==== 测试准备 ====
准备文件：
  * run.sh
  * 甲基化结果文件
  * samplelist.config

----

==== 刷流程脚本 ====
  * **run.sh** (已测试√)

  sh run.sh
  
  run.sh :
  python  /TJPROJ6/NC_BG_SH/personal_dir/liuying/WGBS/Methylation_Pipeline_V7.3.2.qsubname.py  \
	--project X101SC21083023-Z01-J002-B1_Glycine_max,东北农业大学20个大豆全基因组甲基化分析技术服务（委托）合同,X101SC21083023-Z01-J002-B1 \
	--sampleconfig samplelist.config \
	--direction yes \
	--dml yes \
	--datasize 100 \
	--genome /TJPROJ6/NC_BG_SH/shouhou/202205/X101SC21083023-Z01-J002_chongfenxi/reference \
	--gtf /TJPROJ6/NC_BG_SH/shouhou/202205/X101SC21083023-Z01-J002_chongfenxi/reference/genome.gtf \
	--chrlist /TJPROJ6/NC_BG_SH/shouhou/202205/X101SC21083023-Z01-J002_chongfenxi/reference/chrlist \
	--goann /TJPROJ6/NC_BG_SH/shouhou/202205/X101SC21083023-Z01-J002_chongfenxi/reference/go.txt \
	--genenamefile /TJPROJ6/NC_BG_SH/shouhou/202205/X101SC21083023-Z01-J002_chongfenxi/reference/gene.genenames \
	--species gmx \
	--features promoter,exon,intron \
	--name xinxi \
	--yunyingname yunying \
	--HEADCROP 10 \
	--library_type LiBS \
	--queue rnash.q \
	--group DN_0,M_0,DN_10,M_10 \
	--groupname DN_0,M_0,DN_10,M_10 \
	--compare 2:1,3:1,4:3,4:2 \


----

==== 跑流程 ====

  * **将data_release中的CX_report文件链接到2号文件夹每一个样本文件夹中的bismark_result**

  cp DN_0.clean.fq_bismark_bt2_pe.sam_deduplicated_to_representative_sequences_pe.CX_report.txt_sorted.gz 
  2.Map_Methy/DN_0/bismark_result 

  * **投递每个样本文件夹下的dmr_dplit_data.sh(2G 1p)，对每个样本的C位点信息按染色体进行拆分**

  cd  4.DME_Methy/dmr_split/DN_0
  qsub dmr_dplit_data.sh

  * **投递run_DMR_prepare.sh(1G 1p)脚本，生成每个比较组合的dml分析脚本**

  cd 4.DME_Methy/dmr_split
  qsub run_DMR_prepare.sh

  * **本地sh A_vs_B_qsub.sh，自动投递dml分析脚本**

  cd 4.DME_Methy/DN_10_vs_DN_0
  sh DN_10_vs_DN_0_qsub.sh

  * **投递A_vs_B_merge.sh（1G 1p）,合并dml分析结果**

  qsub DN_10_vs_DN_0_merge.sh