===== new miRNA-mRNA联合分析流程=====
  /TJPROJ6/NC_BG_SH/personal_dir/lihang/asso/miRNA_mRNA/new/custom_sRNA_analysis.new.pl
  适用新miRNA流程和ref关联分析

==== 刷流程脚本 ====
** asso.sh **
  perl /TJPROJ6/NC_BG_SH/personal_dir/lihang/asso/miRNA_mRNA/new/custom_sRNA_analysis.new.pl \
	-project  asso \
	-od /TJPROJ6/NC_BG_SH/shouhou/202208/X101SC22053906-Z01-J004_asso \
	-asso  y  \
	-type Ref  \
	-t plant  \
	-mirna /TJPROJ6/NC_BG_SH/shouhou/202208/X101SC22053906-Z01-J004_asso/raw/miRNA/Result_X101SC22053906-Z01-J004_Solanum_lycopersicum/14.DiffExprAnalysis/14.4.DiffExprAnalysis \
	-mrna /TJPROJ6/NC_BG_SH/shouhou/202208/X101SC22053906-Z01-J004_asso/raw/mRNA/Result_X101SC22041739-Z01-J007-B7-16/5.Differential/1.deglist \
	-union /TJPROJ6/NC_BG_SH/shouhou/202208/X101SC22053906-Z01-J004_asso/raw/mRNA/Result_X101SC22041739-Z01-J007-B7-16/5.Differential/3.cluster/diff_uion.xls \
	-mirnacn VirusvsWT \
	-mrnacn VirusvsWT \
	-assotype ref  \
	-pairs /TJPROJ6/NC_BG_SH/shouhou/202208/X101SC22053906-Z01-J004_asso/raw/miRNA/Result_X101SC22053906-Z01-J004_Solanum_lycopersicum/15.miRNA_target/targets_gene.pairs \
	-species sly \
	-refdir /TJPROJ6/GB_TR/reference_data/new_pip/Plant/Solanum_lycopersicum/Solanum_lycopersicum_ncbi_srna/genome/ \
        -description  /TJPROJ6/NC_BG_SH/shouhou/202208/X101SC22053906-Z01-J004_asso/raw/mRNA/Result_X101SC22041739-Z01-J007-B7-16/0.Supfile/gene.xls

===== 测试 =====

脚本路径：
 /TJPROJ6/NC_BG_SH/personal_dir/wangshuai/miRNA-mRNA/ciji
  
测试路径：
  /TJPROJ6/NC_BG_SH/personal_dir/wangshuai/miRNA-mRNA

**[[流程修改日志]]**
----

==== 测试准备 ====
准备文件：
  * miRNA差异文件
  * mRNA差异文件
  * mRNA定量结果文件
  * miRNA和target_gene的结果文件
  * 参考基因组的路径
----

==== 刷流程脚本 ====
  * **run.sh** (已测试√)


  perl /TJPROJ6/NC_BG_SH/script_dir/miRNA-mRNA/custom_sRNA_analysis.pl \#替换kegg注释脚本
  perl  /TJPROJ6/NC_BG_SH/personal_dir/lihang/asso/miRNA_mRNA/custom_sRNA_analysis.pl \
	-project  asso \
	-od  /TJPROJ6/NC_BG_SH/shouhou/202204/X101SC22011429-Z02-J001 \
	-asso  y  \
	-type Ref  \
	-t animal  \
	-mirna /TJPROJ6/NC_BG_SH/shouhou/202204/X101SC22011429-Z02-J001/miRNA/X101SC22011429-Z02-J001-B1-35-Ictalurus_Punetaus_results/12.DiffExprAnalysis/12.4.DiffExprAnalysis \
	-mrna /TJPROJ6/NC_BG_SH/shouhou/202204/X101SC22011429-Z02-J001/mRNA/Result_X101SC22011429-Z01-F001-B1-16/5.Differential/1.deglist \
	-union  /TJPROJ6/NC_BG_SH/shouhou/202204/X101SC22011429-Z02-J001/mRNA/Result_X101SC22011429-Z01-F001-B1-16/4.Quant/1.Count/diff_uion.xls \
	-mirnacn HCDvsCON,BBRvsHCD,BBRvsCON \  #miRNA比较组合的顺序应与mRNA比较组合的顺序一致
	-mrnacn  HCDvsCON,BBRvsHCD,BBRvsCON \  #应与miRNA比较组合的顺序一致
	-assotype ref  \
	-pairs /TJPROJ6/NC_BG_SH/shouhou/202204/X101SC22011429-Z02-J001/miRNA/X101SC22011429-Z02-J001-B1-35-Ictalurus_Punetaus_results/13.miRNA_target/ipu_mature.miranda_targets.pairs \
	-refdir /TJPROJ6/GB_TR/reference_data/Animal/Ictalurus_punctatus/GCF_001660625.1_IpCoco_1.2_sRNA \
	-species  ipu \


----

==== 跑流程 ====

  * **/Association/run_association_analysis.sh &** (已测试√)

  nohup sh run_association_analysis.sh &