----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09c_DiffExp_3_lncRNA_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170 Dataset_Label: G170 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: F_Placebo_TD227 CONDITION_2_NAME: F_CPA_7cycle_TD227 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 : Mon Sep 16 10:47:52 EDT 2019 Running on node : scc-tm4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09c_DiffExp_3_lncRNA_featureCounts Current job ID : 9373946 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/9373946.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G170_M7 Sample_ID: G170_M7 Description: F_Placebo1_TD227 M_Num: M7 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G170_M8 Sample_ID: G170_M8 Description: F_Placebo2_TD227 M_Num: M8 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G170_M9 Sample_ID: G170_M9 Description: F_Placebo3_TD227 M_Num: M9 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: M7M8M9 ------------------------------------------ ------------------------------------------ Sample_DIR: G170_M16 Sample_ID: G170_M16 Description: F_CPA_7cycle10_TD227 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: G170_M17 Sample_ID: G170_M17 Description: F_CPA_7cycle11_TD227 M_Num: M17 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: M16M17 ------------------------------------------ ========================================================== 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 G170_M16_sorted.bam Assigned 14894279 Unassigned_Ambiguity 9702 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3673020 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G170_M17_sorted.bam Assigned 10528327 Unassigned_Ambiguity 6917 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2417089 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G170_M7_sorted.bam Assigned 8457914 Unassigned_Ambiguity 3840 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2312407 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G170_M8_sorted.bam Assigned 13140118 Unassigned_Ambiguity 7022 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3916542 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G170_M9_sorted.bam Assigned 12415372 Unassigned_Ambiguity 6280 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3586100 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 718828 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_CPA_7cycle_TD2270.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_CPA_7cycle_TD2270.summary -rw-r--r-- 1 kkarri waxmanlab 716503 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_CPA_7cycle_TD2271.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_CPA_7cycle_TD2271.summary -rw-r--r-- 1 kkarri waxmanlab 714920 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_Placebo_TD2270.out -rw-r--r-- 1 kkarri waxmanlab 295 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_Placebo_TD2270.summary -rw-r--r-- 1 kkarri waxmanlab 718018 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_Placebo_TD2271.out -rw-r--r-- 1 kkarri waxmanlab 296 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_Placebo_TD2271.summary -rw-r--r-- 1 kkarri waxmanlab 717446 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_Placebo_TD2272.out -rw-r--r-- 1 kkarri waxmanlab 296 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_Placebo_TD2272.summary -rw-r--r-- 1 kkarri waxmanlab 794757 Sep 16 10:47 /scratch/9373946.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/9373946.1.linga/Input/F_CPA_7cycle_TD227: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:47 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:47 .. /scratch/9373946.1.linga/Input/F_Placebo_TD227: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:47 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:47 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R F_Placebo_TD227 F_CPA_7cycle_TD227 3 2 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/9373946.1.linga/Input DiffExp_v2_LncRNA_Exonic_Only exonic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "F_Placebo_TD227" [1] "F_CPA_7cycle_TD227" [1] 3 [1] 2 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/9373946.1.linga/Input" [1] "DiffExp_v2_LncRNA_Exonic_Only" [1] "exonic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] 15558 23 [1] 15558 51 [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/9373946.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_F_Placebo_TD227_F_CPA_7cycle_TD227.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Exonic_Only_F_Placebo_TD227_F_CPA_7cycle_TD227.txt F_CPA_7cycle_TD227_G170_M16M17_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only ========================================================== Comparison_Info: F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R F_CPA_7cycle_TD227_G170_M16M17_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Exonic_Only'_'F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_7cycle_TD227_G170_M16M17_vs_F_Placebo_TD227_G170_M7M8M9_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_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 40 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 36 7 [1] "Check out Up_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt!" Rscript Diff_Genes.R F_CPA_7cycle_TD227_G170_M16M17_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Exonic_Only'_'F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_7cycle_TD227_G170_M16M17_vs_F_Placebo_TD227_G170_M7M8M9_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_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 56 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 40 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt Down_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt LncRNA_Exonic_Only_Counting DiffExp_3f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.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_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt Up_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt LncRNA_Exonic_Only_Counting DiffExp_3f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.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: F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 321 Sep 16 10:48 /scratch/9373946.1.linga/Input/DiffExp_3f_Venn_Tables_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt -rw-r--r-- 1 kkarri waxmanlab 4488166 Sep 16 10:48 /scratch/9373946.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Sep 16 10:47 /scratch/9373946.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 4414 Sep 16 10:48 /scratch/9373946.1.linga/Input/Down_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt -rw-r--r-- 1 kkarri waxmanlab 4432 Sep 16 10:48 /scratch/9373946.1.linga/Input/Down_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt -rw-r--r-- 1 kkarri waxmanlab 718828 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_CPA_7cycle_TD2270.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_CPA_7cycle_TD2270.summary -rw-r--r-- 1 kkarri waxmanlab 716503 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_CPA_7cycle_TD2271.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_CPA_7cycle_TD2271.summary -rw-r--r-- 1 kkarri waxmanlab 2183663 Sep 16 10:48 /scratch/9373946.1.linga/Input/F_CPA_7cycle_TD227_G170_M16M17_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2043641 Sep 16 10:48 /scratch/9373946.1.linga/Input/F_CPA_7cycle_TD227_G170_M16M17_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 714920 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_Placebo_TD2270.out -rw-r--r-- 1 kkarri waxmanlab 295 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_Placebo_TD2270.summary -rw-r--r-- 1 kkarri waxmanlab 718018 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_Placebo_TD2271.out -rw-r--r-- 1 kkarri waxmanlab 296 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_Placebo_TD2271.summary -rw-r--r-- 1 kkarri waxmanlab 717446 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_Placebo_TD2272.out -rw-r--r-- 1 kkarri waxmanlab 296 Sep 16 10:47 /scratch/9373946.1.linga/Input/F_Placebo_TD2272.summary -rw-r--r-- 1 kkarri waxmanlab 3715 Sep 16 10:48 /scratch/9373946.1.linga/Input/Up_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt -rw-r--r-- 1 kkarri waxmanlab 5277 Sep 16 10:48 /scratch/9373946.1.linga/Input/Up_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Sep 16 10:47 /scratch/9373946.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 43589 Sep 16 10:48 /scratch/9373946.1.linga/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40813 Sep 16 10:48 /scratch/9373946.1.linga/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 794757 Sep 16 10:47 /scratch/9373946.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt -rwxr-xr-x 1 kkarri waxmanlab 4968 Sep 16 10:47 /scratch/9373946.1.linga/Input/formatForSegex_ver3.R /scratch/9373946.1.linga/Input/F_CPA_7cycle_TD227: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:47 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:48 .. /scratch/9373946.1.linga/Input/F_Placebo_TD227: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:47 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:48 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Sep 16 10:48 . drwxrwxrwt. 9 root root 4.0K Sep 16 10:47 .. -rw-r--r-- 1 kkarri waxmanlab 132 Sep 16 10:47 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 111 Sep 16 10:47 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Sep 16 10:48 Input -rwxr-xr-x 1 kkarri waxmanlab 13K Sep 16 10:47 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Sep 16 10:47 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 21M drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 10:42 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Sep 16 10:42 .. -rw-r--r-- 1 kkarri waxmanlab 321 Sep 16 10:42 DiffExp_3f_Venn_Tables_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.3M Sep 16 10:42 DiffExp_v2_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.4K Sep 16 10:42 Down_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.4K Sep 16 10:42 Down_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.1M Sep 16 10:42 F_CPA_7cycle_TD227_G170_M16M17_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.0M Sep 16 10:42 F_CPA_7cycle_TD227_G170_M16M17_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.7K Sep 16 10:42 Up_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.2K Sep 16 10:42 Up_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_7cycle_TD227_G170_M16M17_F_Placebo_TD227_G170_M7M8M9_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 43K Sep 16 10:42 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 40K Sep 16 10:42 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Sep 16 10:48:28 EDT 2019 0 minutes and 36 seconds elapsed. ==========================================================