----------------------- 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_4_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: M2WTF CONDITION_2_NAME: M2Ezh12F Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: intronic_only_gene_models_ncRNA_for_counting_lengths.txt COUNT_DIR: LncRNA_Intronic_Only_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_Intronic_Only DiffExp_Index: DiffExp_4g COL_SUFFIX: LncRNA_Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 10 06:21:34 EDT 2020 Running on node : scc-kb8 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_4_lncRNA_featureCounts Current job ID : 3782045 Current job name : Step_08c_DiffExp_4g Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3782045.1.linga Loading required modules... ------------------------------------------ Sample_DIR: M2WTF_1 Sample_ID: M2WTF_1 Description: M2WTF_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: M2WTF_2 Sample_ID: M2WTF_2 Description: M2WTF_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: M2Ezh12F_1 Sample_ID: M2Ezh12F_1 Description: M2Ezh12F_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: M2Ezh12F_2 Sample_ID: M2Ezh12F_2 Description: M2Ezh12F_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: M2Ezh12F_3 Sample_ID: M2Ezh12F_3 Description: M2Ezh12F_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 M_Num_Cond2_List: 123 ------------------------------------------ ========================================================== 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 M2Ezh12F_1_sorted.bam Assigned 4391940 Unassigned_Ambiguity 825558 Unassigned_MultiMapping 0 Unassigned_NoFeatures 24952168 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2Ezh12F_2_sorted.bam Assigned 2235682 Unassigned_Ambiguity 468006 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11711307 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2Ezh12F_3_sorted.bam Assigned 1455874 Unassigned_Ambiguity 419175 Unassigned_MultiMapping 0 Unassigned_NoFeatures 10750534 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2WTF_1_sorted.bam Assigned 2301679 Unassigned_Ambiguity 610124 Unassigned_MultiMapping 0 Unassigned_NoFeatures 12856265 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2WTF_2_sorted.bam Assigned 2224366 Unassigned_Ambiguity 625016 Unassigned_MultiMapping 0 Unassigned_NoFeatures 12374278 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 352988 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2Ezh12F0.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2Ezh12F0.summary -rw-r--r-- 1 kkarri waxmanlab 349472 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2Ezh12F1.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2Ezh12F1.summary -rw-r--r-- 1 kkarri waxmanlab 345882 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2Ezh12F2.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2Ezh12F2.summary -rw-r--r-- 1 kkarri waxmanlab 347874 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2WTF0.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2WTF0.summary -rw-r--r-- 1 kkarri waxmanlab 348095 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2WTF1.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2WTF1.summary -rw-r--r-- 1 kkarri waxmanlab 414633 Mar 10 06:21 /scratch/3782045.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3782045.1.linga/Input/M2Ezh12F: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:21 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:21 .. /scratch/3782045.1.linga/Input/M2WTF: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:21 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:21 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R M2WTF M2Ezh12F 2 3 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/3782045.1.linga/Input DiffExp_v2_LncRNA_Intronic_Only intronic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "M2WTF" [1] "M2Ezh12F" [1] 2 [1] 3 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/3782045.1.linga/Input" [1] "DiffExp_v2_LncRNA_Intronic_Only" [1] "intronic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] "sum1:26375.8029728786" "sum1:29642.4687450495" "sum1:28009.1358589641" [1] "sum2:25526.5836955502" "sum2:27086.211296228" "sum2:27216.7269236359" [4] "sum2:26609.8406384714" [1] 15558 23 [1] 15558 59 [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/3782045.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_M2WTF_M2Ezh12F.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Intronic_Only_M2WTF_M2Ezh12F.txt M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload 1 LncRNA_Intronic_Only Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_LncRNA_Intronic_Only_M2WTF_M2Ezh12F.txt M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload 1 LncRNA_Intronic_Only ========================================================== Comparison_Info: M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Intronic_Only'_'M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_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_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 35 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 30 7 [1] "Check out Up_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt!" Rscript Diff_Genes.R M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Intronic_Only'_'M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_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_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 61 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 42 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt LncRNA_Intronic_Only_Counting DiffExp_4g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_4g" [1] "-----------------" [1] "Down.DESeq.Intronic_Only.HTSeq" [1] "Down.EdgeR.Intronic_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_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt LncRNA_Intronic_Only_Counting DiffExp_4g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_4g" [1] "-----------------" [1] "Up.DESeq.Intronic_Only.HTSeq" [1] "Up.EdgeR.Intronic_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: M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 334 Mar 10 06:22 /scratch/3782045.1.linga/Input/DiffExp_4g_Venn_Tables_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 3855829 Mar 10 06:22 /scratch/3782045.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_M2WTF_M2Ezh12F.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Mar 10 06:21 /scratch/3782045.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 4010 Mar 10 06:22 /scratch/3782045.1.linga/Input/Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 5290 Mar 10 06:22 /scratch/3782045.1.linga/Input/Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 352988 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2Ezh12F0.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2Ezh12F0.summary -rw-r--r-- 1 kkarri waxmanlab 349472 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2Ezh12F1.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2Ezh12F1.summary -rw-r--r-- 1 kkarri waxmanlab 345882 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2Ezh12F2.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2Ezh12F2.summary -rw-r--r-- 1 kkarri waxmanlab 2432585 Mar 10 06:22 /scratch/3782045.1.linga/Input/M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2354795 Mar 10 06:22 /scratch/3782045.1.linga/Input/M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1064779 Mar 10 06:22 /scratch/3782045.1.linga/Input/M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1488904 Mar 10 06:22 /scratch/3782045.1.linga/Input/M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 347874 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2WTF0.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2WTF0.summary -rw-r--r-- 1 kkarri waxmanlab 348095 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2WTF1.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:21 /scratch/3782045.1.linga/Input/M2WTF1.summary -rw-r--r-- 1 kkarri waxmanlab 2996 Mar 10 06:22 /scratch/3782045.1.linga/Input/Up_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 7158 Mar 10 06:22 /scratch/3782045.1.linga/Input/Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Mar 10 06:21 /scratch/3782045.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 44280 Mar 10 06:22 /scratch/3782045.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 41857 Mar 10 06:22 /scratch/3782045.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 4968 Mar 10 06:21 /scratch/3782045.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Mar 10 06:21 /scratch/3782045.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 414633 Mar 10 06:21 /scratch/3782045.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3782045.1.linga/Input/M2Ezh12F: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:21 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:22 .. /scratch/3782045.1.linga/Input/M2WTF: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:21 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:22 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Mar 10 06:22 . drwxrwxrwt. 18 root root 4.0K Mar 10 06:21 .. -rw-r--r-- 1 kkarri waxmanlab 81 Mar 10 06:21 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 132 Mar 10 06:21 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 10 06:22 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Mar 10 06:21 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Mar 10 06:21 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 19M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 10 06:14 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 10 06:14 .. -rw-r--r-- 1 kkarri waxmanlab 334 Mar 10 06:14 DiffExp_4g_Venn_Tables_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.7M Mar 10 06:14 DiffExp_v2_LncRNA_Intronic_Only_M2WTF_M2Ezh12F_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.0K Mar 10 06:14 Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.2K Mar 10 06:14 Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.4M Mar 10 06:14 M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Mar 10 06:14 M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.1M Mar 10 06:14 M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.5M Mar 10 06:14 M2Ezh12F_GSE118757_123_vs_M2WTF_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.0K Mar 10 06:14 Up_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 7.0K Mar 10 06:14 Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12F_GSE118757_123_M2WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 44K Mar 10 06:14 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 41K Mar 10 06:14 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Tue Mar 10 06:22:29 EDT 2020 0 minutes and 55 seconds elapsed. ==========================================================