export PYTHONPATH="" unset PERL5LIB export PATH=/TJPROJ2/GB/PUBLIC/software/GB_TR/mRNA/miniconda3/envs/immuno/bin:$PATH mkdir -p /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/1.Estimate python /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/modify_couny.py /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Quant/gene_fpkm.xls /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/gene_fpkm_name.xls Rscript /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/estimate.R --fpkm /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/gene_fpkm_name.xls --outdir /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/1.Estimate --condition /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Quant/condition.xls --sample Sham_1,Sham_2,Sham_3,IRI_1,IRI_2,IRI_3,TA_1,TA_2,TA_3 /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/pdf_to_png --indir /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/1.Estimate mkdir -p /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell Rscript /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/Xcell.R --fpkm /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/gene_fpkm_name.xls --outdir /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell python /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/modify_xCell_RNAseq.py /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell/xcell_all.xls /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell/xCell_interval.xls /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell/xcell_select.xls Rscript /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/bar_for_Xcell.R /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell/xCell_interval.xls /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/pdf_to_png --indir /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell mkdir -p /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/3.Immunophenogram cd /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/3.Immunophenogram python /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/count_TPM.py /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Quant/gene_count.xls /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/3.Immunophenogram/log2tpm.xls Rscript /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/IPS.R /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/3.Immunophenogram/log2tpm.xls /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/pipline1.1/bin/Immuno/Immunophenogram-master/IPS_genes.txt rm /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/gene_fpkm_name.xls /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/1.Estimate/fpkm.gct /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/1.Estimate/fpkm_out.gct /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell/xCell_interval.xls /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/pdf_to_png --indir /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/3.Immunophenogram