----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_1_lncRNA_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana Dataset_Label: GSE118757 ANNOTATION_FILE_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt CONDITION_1_NAME: WTF CONDITION_2_NAME: Ezh12F Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: exonic_only_gene_models_ncRNA_for_counting_lengths.txt COUNT_DIR: LncRNA_Exonic_Only_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_Exonic_Only DiffExp_Index: DiffExp_1f COL_SUFFIX: LncRNA_Exonic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Mar 13 13:40:07 EDT 2020 Running on node : scc-tk2 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_1_lncRNA_featureCounts Current job ID : 3818270 Current job name : Step_08c_DiffExp_1f Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3818270.1.linga Loading required modules... ------------------------------------------ Sample_DIR: WTF_1 Sample_ID: WTF_1 Description: WTF_1 M_Num: 1 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: WTF_2 Sample_ID: WTF_2 Description: WTF_2 M_Num: 2 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder M_Num_Cond1_List: 12 ------------------------------------------ ------------------------------------------ Sample_DIR: Ezh12F_1 Sample_ID: Ezh12F_1 Description: Ezh12F_1 M_Num: 1 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_2 Sample_ID: Ezh12F_2 Description: Ezh12F_2 M_Num: 2 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_3 Sample_ID: Ezh12F_3 Description: Ezh12F_3 M_Num: 3 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_4 Sample_ID: Ezh12F_4 Description: Ezh12F_4 M_Num: 4 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_5 Sample_ID: Ezh12F_5 Description: Ezh12F_5 M_Num: 5 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder M_Num_Cond2_List: 12345 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 2 NUM_REP_CONDITION1: 2 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status Ezh12F_1_sorted.bam Assigned 4882498 Unassigned_Ambiguity 911628 Unassigned_MultiMapping 0 Unassigned_NoFeatures 5539134 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12F_2_sorted.bam Assigned 5852543 Unassigned_Ambiguity 1157687 Unassigned_MultiMapping 0 Unassigned_NoFeatures 5930061 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12F_3_sorted.bam Assigned 6104847 Unassigned_Ambiguity 1246607 Unassigned_MultiMapping 0 Unassigned_NoFeatures 5197098 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12F_4_sorted.bam Assigned 6956975 Unassigned_Ambiguity 1390008 Unassigned_MultiMapping 0 Unassigned_NoFeatures 5059205 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12F_5_sorted.bam Assigned 5569778 Unassigned_Ambiguity 1052553 Unassigned_MultiMapping 0 Unassigned_NoFeatures 5298484 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status WTF_1_sorted.bam Assigned 7159762 Unassigned_Ambiguity 1566398 Unassigned_MultiMapping 0 Unassigned_NoFeatures 6507841 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status WTF_2_sorted.bam Assigned 6861750 Unassigned_Ambiguity 1461415 Unassigned_MultiMapping 0 Unassigned_NoFeatures 5804922 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 709469 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F0.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F0.summary -rw-r--r-- 1 kkarri waxmanlab 709969 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F1.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F1.summary -rw-r--r-- 1 kkarri waxmanlab 709847 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F2.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F2.summary -rw-r--r-- 1 kkarri waxmanlab 710630 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F3.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F3.summary -rw-r--r-- 1 kkarri waxmanlab 709442 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F4.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F4.summary -rw-r--r-- 1 kkarri waxmanlab 709838 Mar 13 13:40 /scratch/3818270.1.linga/Input/WTF0.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 13 13:40 /scratch/3818270.1.linga/Input/WTF0.summary -rw-r--r-- 1 kkarri waxmanlab 709747 Mar 13 13:40 /scratch/3818270.1.linga/Input/WTF1.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 13 13:40 /scratch/3818270.1.linga/Input/WTF1.summary -rw-r--r-- 1 kkarri waxmanlab 794757 Mar 13 13:40 /scratch/3818270.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3818270.1.linga/Input/Ezh12F: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 13 13:40 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 13 13:40 .. /scratch/3818270.1.linga/Input/WTF: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 13 13:40 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 13 13:40 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WTF Ezh12F 2 5 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/3818270.1.linga/Input DiffExp_v2_LncRNA_Exonic_Only exonic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WTF" [1] "Ezh12F" [1] 2 [1] 5 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/3818270.1.linga/Input" [1] "DiffExp_v2_LncRNA_Exonic_Only" [1] "exonic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] "sum1:201265.249026398" "sum1:209876.373755925" "sum1:205570.811391162" [1] "sum2:173019.818610523" "sum2:179698.888748114" "sum2:204564.062240827" [4] "sum2:228590.24097941" "sum2:193575.64906352" "sum2:195889.731928479" [1] 15558 23 [1] 15558 67 [1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" [1] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" [10] "chr19" [1] "chrX" "chrY" [1] "output file is in: /scratch/3818270.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_WTF_Ezh12F.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Exonic_Only_WTF_Ezh12F.txt Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_LncRNA_Exonic_Only_WTF_Ezh12F.txt Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only ========================================================== Comparison_Info: Ezh12F_GSE118757_12345_WTF_GSE118757_12 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Exonic_Only'_'Ezh12F_GSE118757_12345_WTF_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 36 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 34 7 [1] "Check out Up_Genes_DESeq_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt!" Rscript Diff_Genes.R Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Exonic_Only'_'Ezh12F_GSE118757_12345_WTF_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 37 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 64 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt Down_Genes_EdgeR_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt LncRNA_Exonic_Only_Counting DiffExp_1f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1f" [1] "-----------------" [1] "Down.DESeq.Exonic_Only.HTSeq" [1] "Down.EdgeR.Exonic_Only.HTSeq" null device 1 [1] "Removing VennDiagram*.log files" [1] "Check out Venn diagram and Count.Table!" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt Up_Genes_EdgeR_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt LncRNA_Exonic_Only_Counting DiffExp_1f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1f" [1] "-----------------" [1] "Up.DESeq.Exonic_Only.HTSeq" [1] "Up.EdgeR.Exonic_Only.HTSeq" null device 1 [1] "Removing VennDiagram*.log files" [1] "Check out Venn diagram and Count.Table!" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- Comparison_Info: Ezh12F_GSE118757_12345_WTF_GSE118757_12 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 321 Mar 13 13:40 /scratch/3818270.1.linga/Input/DiffExp_1f_Venn_Tables_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 5923509 Mar 13 13:40 /scratch/3818270.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_WTF_Ezh12F.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Mar 13 13:40 /scratch/3818270.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 3577 Mar 13 13:40 /scratch/3818270.1.linga/Input/Down_Genes_DESeq_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 7157 Mar 13 13:40 /scratch/3818270.1.linga/Input/Down_Genes_EdgeR_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 709469 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F0.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F0.summary -rw-r--r-- 1 kkarri waxmanlab 709969 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F1.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F1.summary -rw-r--r-- 1 kkarri waxmanlab 709847 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F2.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F2.summary -rw-r--r-- 1 kkarri waxmanlab 710630 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F3.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F3.summary -rw-r--r-- 1 kkarri waxmanlab 709442 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F4.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F4.summary -rw-r--r-- 1 kkarri waxmanlab 3194909 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 4050599 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1675105 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 3417313 Mar 13 13:40 /scratch/3818270.1.linga/Input/Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 6634 Mar 13 13:40 /scratch/3818270.1.linga/Input/Up_Genes_DESeq_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 8880 Mar 13 13:40 /scratch/3818270.1.linga/Input/Up_Genes_EdgeR_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Mar 13 13:40 /scratch/3818270.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 43221 Mar 13 13:40 /scratch/3818270.1.linga/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 42937 Mar 13 13:40 /scratch/3818270.1.linga/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 709838 Mar 13 13:40 /scratch/3818270.1.linga/Input/WTF0.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 13 13:40 /scratch/3818270.1.linga/Input/WTF0.summary -rw-r--r-- 1 kkarri waxmanlab 709747 Mar 13 13:40 /scratch/3818270.1.linga/Input/WTF1.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 13 13:40 /scratch/3818270.1.linga/Input/WTF1.summary -rw-r--r-- 1 kkarri waxmanlab 794757 Mar 13 13:40 /scratch/3818270.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt -rwxr-xr-x 1 kkarri waxmanlab 4968 Mar 13 13:40 /scratch/3818270.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Mar 13 13:40 /scratch/3818270.1.linga/Input/formatForSegex_ver4.R /scratch/3818270.1.linga/Input/Ezh12F: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 13 13:40 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 13 13:40 .. /scratch/3818270.1.linga/Input/WTF: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 13 13:40 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 13 13:40 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Mar 13 13:40 . drwxrwxrwt. 16 root root 4.0K Mar 13 13:40 .. -rw-r--r-- 1 kkarri waxmanlab 69 Mar 13 13:40 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 168 Mar 13 13:40 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 13 13:40 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Mar 13 13:40 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Mar 13 13:40 ncRNA_output_filtered_final_gene.txt ========================================================== Re-naming files in OUTPUT_DIR Need to append the COUNT_PROGRAM name to all output files List files in OUTPUT_DIR total 30M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 13 13:33 . drwxr-xr-x 6 kkarri waxmanlab 4.0K Mar 13 13:32 .. -rw-r--r-- 1 kkarri waxmanlab 321 Mar 13 13:33 DiffExp_1f_Venn_Tables_Ezh12F_GSE118757_12345_WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.7M Mar 13 13:33 DiffExp_v2_LncRNA_Exonic_Only_WTF_Ezh12F_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.5K Mar 13 13:33 Down_Genes_DESeq_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 7.0K Mar 13 13:33 Down_Genes_EdgeR_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 13:33 Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.9M Mar 13 13:33 Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M Mar 13 13:33 Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.3M Mar 13 13:33 Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 6.5K Mar 13 13:33 Up_Genes_DESeq_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 8.7K Mar 13 13:33 Up_Genes_EdgeR_LncRNA_Exonic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 43K Mar 13 13:33 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 42K Mar 13 13:33 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Fri Mar 13 13:40:57 EDT 2020 0 minutes and 50 seconds elapsed. ==========================================================