----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New_Env_PCA/Scripts/09c_DiffExp_3_lncRNA_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New Dataset_Label: G123 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: Female_3h_Vehicle_G123_M1M10 CONDITION_2_NAME: Female_3h_TCPOBOP_G123_M11M12 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_3f COL_SUFFIX: LncRNA_Exonic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed Feb 27 16:28:59 EST 2019 Running on node : scc-tm1 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New_Env_PCA/Scripts/09c_DiffExp_3_lncRNA_featureCounts Current job ID : 3234872 Current job name : Step_09c_DiffExp_3f Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3234872.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G123_M9 Sample_ID: G123_M1 Description: Female_3h_Vehicle_1 M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G123_M10 Sample_ID: G123_M10 Description: Female_3h_Vehicle_2 M_Num: M10 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: M1M10 ------------------------------------------ ------------------------------------------ Sample_DIR: G123_M11 Sample_ID: G123_M11 Description: Female_3h_TCPOBOP_1 M_Num: M11 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G123_M12 Sample_ID: G123_M12 Description: Female_3h_TCPOBOP_2 M_Num: M12 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: M11M12 ------------------------------------------ ========================================================== 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 G123_M11_sorted.bam Assigned 6018968 Unassigned_Ambiguity 19168 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2490804 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G123_M12_sorted.bam Assigned 7701248 Unassigned_Ambiguity 24308 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3412785 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G123_M10_sorted.bam Assigned 7562997 Unassigned_Ambiguity 24357 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3123969 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G123_M1_sorted.bam Assigned 7649854 Unassigned_Ambiguity 21818 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3487062 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 712679 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_TCPOBOP_G123_M11M120.out -rw-r--r-- 1 kkarri waxmanlab 297 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_TCPOBOP_G123_M11M120.summary -rw-r--r-- 1 kkarri waxmanlab 714648 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_TCPOBOP_G123_M11M121.out -rw-r--r-- 1 kkarri waxmanlab 297 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_TCPOBOP_G123_M11M121.summary -rw-r--r-- 1 kkarri waxmanlab 714421 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_Vehicle_G123_M1M100.out -rw-r--r-- 1 kkarri waxmanlab 297 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_Vehicle_G123_M1M100.summary -rw-r--r-- 1 kkarri waxmanlab 714957 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_Vehicle_G123_M1M101.out -rw-r--r-- 1 kkarri waxmanlab 296 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_Vehicle_G123_M1M101.summary -rw-r--r-- 1 kkarri waxmanlab 794757 Feb 27 16:28 /scratch/3234872.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3234872.1.linga/Input/Female_3h_TCPOBOP_G123_M11M12: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Feb 27 16:28 . drwxr-xr-x 4 kkarri waxmanlab 4096 Feb 27 16:28 .. /scratch/3234872.1.linga/Input/Female_3h_Vehicle_G123_M1M10: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Feb 27 16:28 . drwxr-xr-x 4 kkarri waxmanlab 4096 Feb 27 16:28 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Female_3h_Vehicle_G123_M1M10 Female_3h_TCPOBOP_G123_M11M12 2 2 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/3234872.1.linga/Input DiffExp_v2_LncRNA_Exonic_Only exonic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Female_3h_Vehicle_G123_M1M10" [1] "Female_3h_TCPOBOP_G123_M11M12" [1] 2 [1] 2 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/3234872.1.linga/Input" [1] "DiffExp_v2_LncRNA_Exonic_Only" [1] "exonic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] 15558 23 [1] 15558 50 [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/3234872.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_Female_3h_Vehicle_G123_M1M10_Female_3h_TCPOBOP_G123_M11M12.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Exonic_Only_Female_3h_Vehicle_G123_M1M10_Female_3h_TCPOBOP_G123_M11M12.txt Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_vs_Female_3h_Vehicle_G123_M1M10_G123_M1M10_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_Female_3h_Vehicle_G123_M1M10_Female_3h_TCPOBOP_G123_M11M12.txt Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_vs_Female_3h_Vehicle_G123_M1M10_G123_M1M10_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only Fatal error: cannot open file 'formatForSegex_ver4.R': No such file or directory ========================================================== Comparison_Info: Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_vs_Female_3h_Vehicle_G123_M1M10_G123_M1M10_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Exonic_Only'_'Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_vs_Female_3h_Vehicle_G123_M1M10_G123_M1M10_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_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 17 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 10 7 [1] "Check out Up_Genes_DESeq_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt!" Rscript Diff_Genes.R Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_vs_Female_3h_Vehicle_G123_M1M10_G123_M1M10_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Exonic_Only'_'Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_vs_Female_3h_Vehicle_G123_M1M10_G123_M1M10_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_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 42 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 22 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt Down_Genes_EdgeR_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt LncRNA_Exonic_Only_Counting DiffExp_3f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3f" [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_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt Up_Genes_EdgeR_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt LncRNA_Exonic_Only_Counting DiffExp_3f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3f" [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: Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 321 Feb 27 16:29 /scratch/3234872.1.linga/Input/DiffExp_3f_Venn_Tables_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt -rw-r--r-- 1 kkarri waxmanlab 4929641 Feb 27 16:29 /scratch/3234872.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_Female_3h_Vehicle_G123_M1M10_Female_3h_TCPOBOP_G123_M11M12.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Feb 27 16:28 /scratch/3234872.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 1021 Feb 27 16:29 /scratch/3234872.1.linga/Input/Down_Genes_DESeq_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt -rw-r--r-- 1 kkarri waxmanlab 2031 Feb 27 16:29 /scratch/3234872.1.linga/Input/Down_Genes_EdgeR_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt -rw-r--r-- 1 kkarri waxmanlab 712679 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_TCPOBOP_G123_M11M120.out -rw-r--r-- 1 kkarri waxmanlab 297 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_TCPOBOP_G123_M11M120.summary -rw-r--r-- 1 kkarri waxmanlab 714648 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_TCPOBOP_G123_M11M121.out -rw-r--r-- 1 kkarri waxmanlab 297 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_TCPOBOP_G123_M11M121.summary -rw-r--r-- 1 kkarri waxmanlab 3179399 Feb 27 16:29 /scratch/3234872.1.linga/Input/Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_vs_Female_3h_Vehicle_G123_M1M10_G123_M1M10_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 4003973 Feb 27 16:29 /scratch/3234872.1.linga/Input/Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_vs_Female_3h_Vehicle_G123_M1M10_G123_M1M10_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 714421 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_Vehicle_G123_M1M100.out -rw-r--r-- 1 kkarri waxmanlab 297 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_Vehicle_G123_M1M100.summary -rw-r--r-- 1 kkarri waxmanlab 714957 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_Vehicle_G123_M1M101.out -rw-r--r-- 1 kkarri waxmanlab 296 Feb 27 16:28 /scratch/3234872.1.linga/Input/Female_3h_Vehicle_G123_M1M101.summary -rw-r--r-- 1 kkarri waxmanlab 3262 Feb 27 16:29 /scratch/3234872.1.linga/Input/Up_Genes_DESeq_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt -rw-r--r-- 1 kkarri waxmanlab 9757 Feb 27 16:29 /scratch/3234872.1.linga/Input/Up_Genes_EdgeR_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Feb 27 16:28 /scratch/3234872.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 39804 Feb 27 16:29 /scratch/3234872.1.linga/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 38117 Feb 27 16:29 /scratch/3234872.1.linga/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 794757 Feb 27 16:28 /scratch/3234872.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt -rwxr-xr-x 1 kkarri waxmanlab 4968 Feb 27 16:28 /scratch/3234872.1.linga/Input/formatForSegex_ver3.R /scratch/3234872.1.linga/Input/Female_3h_TCPOBOP_G123_M11M12: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Feb 27 16:28 . drwxr-xr-x 4 kkarri waxmanlab 4096 Feb 27 16:29 .. /scratch/3234872.1.linga/Input/Female_3h_Vehicle_G123_M1M10: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Feb 27 16:28 . drwxr-xr-x 4 kkarri waxmanlab 4096 Feb 27 16:29 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Feb 27 16:29 . drwxrwxrwt. 15 root root 20K Feb 27 16:28 .. -rw-r--r-- 1 kkarri waxmanlab 107 Feb 27 16:28 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 109 Feb 27 16:28 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Feb 27 16:29 Input -rwxr-xr-x 1 kkarri waxmanlab 14K Feb 27 16:28 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Feb 27 16:28 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 11M drwxr-sr-x 2 kkarri waxmanlab 32K Feb 27 16:29 . drwxr-sr-x 7 kkarri waxmanlab 32K Feb 27 16:28 .. -rw-r--r-- 1 kkarri waxmanlab 321 Feb 27 16:29 DiffExp_3f_Venn_Tables_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.8M Feb 27 16:29 DiffExp_v2_LncRNA_Exonic_Only_Female_3h_Vehicle_G123_M1M10_Female_3h_TCPOBOP_G123_M11M12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1021 Feb 27 16:29 Down_Genes_DESeq_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.0K Feb 27 16:29 Down_Genes_EdgeR_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.1M Feb 27 16:29 Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_vs_Female_3h_Vehicle_G123_M1M10_G123_M1M10_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.9M Feb 27 16:29 Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_vs_Female_3h_Vehicle_G123_M1M10_G123_M1M10_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.2K Feb 27 16:29 Up_Genes_DESeq_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 9.6K Feb 27 16:29 Up_Genes_EdgeR_LncRNA_Exonic_Only_Female_3h_TCPOBOP_G123_M11M12_G123_M11M12_Female_3h_Vehicle_G123_M1M10_G123_M1M10_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 39K Feb 27 16:29 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 38K Feb 27 16:29 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Wed Feb 27 16:29:35 EST 2019 0 minutes and 36 seconds elapsed. ==========================================================