----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/08c_DiffExp_1_lncRNA_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion Dataset_Label: LZ 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: NoInf_WT CONDITION_2_NAME: NoInf_KO 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 May 11 18:40:31 EDT 2018 Running on node : scc-wa3 Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/08c_DiffExp_1_lncRNA_featureCounts Current job ID : 6179920 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/6179920.1.w-long Loading required modules... ------------------------------------------ Sample_DIR: LZ_M13 Sample_ID: LZ_M13 Description: NoInf_WT1 M_Num: M13 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: LZ_M14 Sample_ID: LZ_M14 Description: NoInf_WT2 M_Num: M14 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: LZ_M15 Sample_ID: LZ_M15 Description: NoInf_WT3 M_Num: M15 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: M13M14M15 ------------------------------------------ ------------------------------------------ Sample_DIR: LZ_M16 Sample_ID: LZ_M16 Description: NoInf_KO1 M_Num: M16 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: LZ_M17 Sample_ID: LZ_M17 Description: NoInf_KO2 M_Num: M17 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: LZ_M18 Sample_ID: LZ_M18 Description: NoInf_KO3 M_Num: M18 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: M16M17M18 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 3 NUM_REP_CONDITION1: 3 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status LZ_M16_sorted.bam Assigned 7089673 Unassigned_Ambiguity 0 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2322408 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M17_sorted.bam Assigned 8064021 Unassigned_Ambiguity 3 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2838523 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M18_sorted.bam Assigned 6464766 Unassigned_Ambiguity 1 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2570499 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M13_sorted.bam Assigned 10050075 Unassigned_Ambiguity 0 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3766204 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M14_sorted.bam Assigned 9156786 Unassigned_Ambiguity 0 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3407914 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M15_sorted.bam Assigned 8048557 Unassigned_Ambiguity 1 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3103099 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 710129 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 291 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_KO0.summary -rw-r--r-- 1 kkarri waxmanlab 710820 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 291 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_KO1.summary -rw-r--r-- 1 kkarri waxmanlab 709982 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 291 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_KO2.summary -rw-r--r-- 1 kkarri waxmanlab 712184 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_WT0.out -rw-r--r-- 1 kkarri waxmanlab 292 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_WT0.summary -rw-r--r-- 1 kkarri waxmanlab 711657 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_WT1.out -rw-r--r-- 1 kkarri waxmanlab 291 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_WT1.summary -rw-r--r-- 1 kkarri waxmanlab 710947 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_WT2.out -rw-r--r-- 1 kkarri waxmanlab 291 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_WT2.summary -rw-r--r-- 1 kkarri waxmanlab 794757 May 11 18:40 /scratch/6179920.1.w-long/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/6179920.1.w-long/Input/NoInf_KO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 11 18:40 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 11 18:40 .. /scratch/6179920.1.w-long/Input/NoInf_WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 11 18:40 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 11 18:40 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R NoInf_WT NoInf_KO 3 3 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/6179920.1.w-long/Input DiffExp_v2_LncRNA_Exonic_Only exonic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "NoInf_WT" [1] "NoInf_KO" [1] 3 [1] 3 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/6179920.1.w-long/Input" [1] "DiffExp_v2_LncRNA_Exonic_Only" [1] "exonic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] 15558 23 [1] 15558 54 [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/6179920.1.w-long/Input/DiffExp_v2_LncRNA_Exonic_Only_NoInf_WT_NoInf_KO.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Exonic_Only_NoInf_WT_NoInf_KO.txt NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only ========================================================== Comparison_Info: NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Exonic_Only'_'NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_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_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 6 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 12 7 [1] "Check out Up_Genes_DESeq_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt!" Rscript Diff_Genes.R NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Exonic_Only'_'NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_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_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 19 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 26 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt Down_Genes_EdgeR_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt LncRNA_Exonic_Only_Counting DiffExp_1f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.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_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt Up_Genes_EdgeR_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt LncRNA_Exonic_Only_Counting DiffExp_1f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.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: NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 321 May 11 18:41 /scratch/6179920.1.w-long/Input/DiffExp_1f_Venn_Tables_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt -rw-r--r-- 1 kkarri waxmanlab 4602500 May 11 18:41 /scratch/6179920.1.w-long/Input/DiffExp_v2_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 May 11 18:40 /scratch/6179920.1.w-long/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 1247 May 11 18:41 /scratch/6179920.1.w-long/Input/Down_Genes_DESeq_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt -rw-r--r-- 1 kkarri waxmanlab 2702 May 11 18:41 /scratch/6179920.1.w-long/Input/Down_Genes_EdgeR_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt -rw-r--r-- 1 kkarri waxmanlab 710129 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 291 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_KO0.summary -rw-r--r-- 1 kkarri waxmanlab 710820 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 291 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_KO1.summary -rw-r--r-- 1 kkarri waxmanlab 709982 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 291 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_KO2.summary -rw-r--r-- 1 kkarri waxmanlab 1872486 May 11 18:41 /scratch/6179920.1.w-long/Input/NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1950276 May 11 18:41 /scratch/6179920.1.w-long/Input/NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 712184 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_WT0.out -rw-r--r-- 1 kkarri waxmanlab 292 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_WT0.summary -rw-r--r-- 1 kkarri waxmanlab 711657 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_WT1.out -rw-r--r-- 1 kkarri waxmanlab 291 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_WT1.summary -rw-r--r-- 1 kkarri waxmanlab 710947 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_WT2.out -rw-r--r-- 1 kkarri waxmanlab 291 May 11 18:40 /scratch/6179920.1.w-long/Input/NoInf_WT2.summary -rw-r--r-- 1 kkarri waxmanlab 736 May 11 18:41 /scratch/6179920.1.w-long/Input/Up_Genes_DESeq_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt -rw-r--r-- 1 kkarri waxmanlab 1998 May 11 18:41 /scratch/6179920.1.w-long/Input/Up_Genes_EdgeR_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 May 11 18:40 /scratch/6179920.1.w-long/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 40239 May 11 18:41 /scratch/6179920.1.w-long/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 37309 May 11 18:41 /scratch/6179920.1.w-long/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 794757 May 11 18:40 /scratch/6179920.1.w-long/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt -rwxr-xr-x 1 kkarri waxmanlab 4968 May 11 18:40 /scratch/6179920.1.w-long/Input/formatForSegex_ver3.R /scratch/6179920.1.w-long/Input/NoInf_KO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 11 18:40 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 11 18:41 .. /scratch/6179920.1.w-long/Input/NoInf_WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 11 18:40 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 11 18:41 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K May 11 18:41 . drwxrwxrwt. 29 root root 48K May 11 18:40 .. -rw-r--r-- 1 kkarri waxmanlab 105 May 11 18:40 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 105 May 11 18:40 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K May 11 18:41 Input -rwxr-xr-x 1 kkarri waxmanlab 13K May 11 18:40 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M May 11 18:40 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 5.1M drwxr-sr-x 2 kkarri waxmanlab 32K May 11 18:41 . drwxr-sr-x 7 kkarri waxmanlab 32K May 11 18:40 .. -rw-r--r-- 1 kkarri waxmanlab 321 May 11 18:41 DiffExp_1f_Venn_Tables_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.4M May 11 18:41 DiffExp_v2_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.3K May 11 18:41 Down_Genes_DESeq_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.7K May 11 18:41 Down_Genes_EdgeR_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.8M May 11 18:41 NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.9M May 11 18:41 NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 736 May 11 18:41 Up_Genes_DESeq_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.0K May 11 18:41 Up_Genes_EdgeR_LncRNA_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 40K May 11 18:41 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 37K May 11 18:41 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Fri May 11 18:41:18 EDT 2018 0 minutes and 47 seconds elapsed. ==========================================================