售后

/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

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

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

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

—-

• 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 \

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

nohup sh run_association_analysis.sh &