----------------------- 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_5_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: M2WTM CONDITION_2_NAME: M2Ezh12M 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_5g COL_SUFFIX: LncRNA_Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 10 06:22:51 EDT 2020 Running on node : scc-tk3 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_5_lncRNA_featureCounts Current job ID : 3782049 Current job name : Step_08c_DiffExp_5g Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3782049.1.linga Loading required modules... ------------------------------------------ Sample_DIR: M2WTM_1 Sample_ID: M2WTM_1 Description: M2WTM_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: M2WTM_2 Sample_ID: M2WTM_2 Description: M2WTM_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: M2Ezh12M_1 Sample_ID: M2Ezh12M_1 Description: M2Ezh12M_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: M2Ezh12M_2 Sample_ID: M2Ezh12M_2 Description: M2Ezh12M_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: M2Ezh12M_3 Sample_ID: M2Ezh12M_3 Description: M2Ezh12M_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 M2Ezh12M_1_sorted.bam Assigned 2623543 Unassigned_Ambiguity 447397 Unassigned_MultiMapping 0 Unassigned_NoFeatures 10749292 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2Ezh12M_2_sorted.bam Assigned 2323792 Unassigned_Ambiguity 534847 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11072122 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2Ezh12M_3_sorted.bam Assigned 980171 Unassigned_Ambiguity 249058 Unassigned_MultiMapping 0 Unassigned_NoFeatures 6070043 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2WTM_1_sorted.bam Assigned 1341939 Unassigned_Ambiguity 833454 Unassigned_MultiMapping 0 Unassigned_NoFeatures 10493073 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2WTM_2_sorted.bam Assigned 1394741 Unassigned_Ambiguity 822479 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11310168 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 350995 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2Ezh12M0.summary -rw-r--r-- 1 kkarri waxmanlab 349322 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2Ezh12M1.summary -rw-r--r-- 1 kkarri waxmanlab 344514 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2Ezh12M2.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2Ezh12M2.summary -rw-r--r-- 1 kkarri waxmanlab 344068 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2WTM0.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2WTM0.summary -rw-r--r-- 1 kkarri waxmanlab 344017 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2WTM1.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2WTM1.summary -rw-r--r-- 1 kkarri waxmanlab 414633 Mar 10 06:22 /scratch/3782049.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3782049.1.linga/Input/M2Ezh12M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:22 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:22 .. /scratch/3782049.1.linga/Input/M2WTM: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:22 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:22 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R M2WTM M2Ezh12M 2 3 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/3782049.1.linga/Input DiffExp_v2_LncRNA_Intronic_Only intronic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "M2WTM" [1] "M2Ezh12M" [1] 2 [1] 3 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/3782049.1.linga/Input" [1] "DiffExp_v2_LncRNA_Intronic_Only" [1] "intronic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] "sum1:31177.0918087022" "sum1:27305.8564091849" "sum1:29241.4741089435" [1] "sum2:28628.3949938226" "sum2:22836.5738084052" "sum2:25832.6520029308" [4] "sum2:25765.8736017196" [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/3782049.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_M2WTM_M2Ezh12M.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Intronic_Only_M2WTM_M2Ezh12M.txt M2Ezh12M_GSE118757_123_vs_M2WTM_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_M2WTM_M2Ezh12M.txt M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload 1 LncRNA_Intronic_Only ========================================================== Comparison_Info: M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Intronic_Only'_'M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2Ezh12M_GSE118757_123_vs_M2WTM_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_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 21 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 126 7 [1] "Check out Up_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt!" Rscript Diff_Genes.R M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Intronic_Only'_'M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2Ezh12M_GSE118757_123_vs_M2WTM_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_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 31 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 156 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt LncRNA_Intronic_Only_Counting DiffExp_5g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_5g" [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_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt LncRNA_Intronic_Only_Counting DiffExp_5g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_5g" [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: M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 336 Mar 10 06:23 /scratch/3782049.1.linga/Input/DiffExp_5g_Venn_Tables_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 3816386 Mar 10 06:23 /scratch/3782049.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_M2WTM_M2Ezh12M.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Mar 10 06:22 /scratch/3782049.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 15044 Mar 10 06:23 /scratch/3782049.1.linga/Input/Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 20760 Mar 10 06:23 /scratch/3782049.1.linga/Input/Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 350995 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2Ezh12M0.summary -rw-r--r-- 1 kkarri waxmanlab 349322 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2Ezh12M1.summary -rw-r--r-- 1 kkarri waxmanlab 344514 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2Ezh12M2.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2Ezh12M2.summary -rw-r--r-- 1 kkarri waxmanlab 2245889 Mar 10 06:23 /scratch/3782049.1.linga/Input/M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2479259 Mar 10 06:23 /scratch/3782049.1.linga/Input/M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 952790 Mar 10 06:23 /scratch/3782049.1.linga/Input/M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1595508 Mar 10 06:23 /scratch/3782049.1.linga/Input/M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 344068 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2WTM0.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2WTM0.summary -rw-r--r-- 1 kkarri waxmanlab 344017 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2WTM1.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:22 /scratch/3782049.1.linga/Input/M2WTM1.summary -rw-r--r-- 1 kkarri waxmanlab 1895 Mar 10 06:23 /scratch/3782049.1.linga/Input/Up_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 3134 Mar 10 06:23 /scratch/3782049.1.linga/Input/Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Mar 10 06:22 /scratch/3782049.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 43725 Mar 10 06:23 /scratch/3782049.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 41585 Mar 10 06:23 /scratch/3782049.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 4968 Mar 10 06:22 /scratch/3782049.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Mar 10 06:22 /scratch/3782049.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 414633 Mar 10 06:22 /scratch/3782049.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3782049.1.linga/Input/M2Ezh12M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:22 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:23 .. /scratch/3782049.1.linga/Input/M2WTM: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:22 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:23 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Mar 10 06:23 . drwxrwxrwt. 17 root root 4.0K Mar 10 06:23 .. -rw-r--r-- 1 kkarri waxmanlab 81 Mar 10 06:22 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 132 Mar 10 06:22 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 10 06:23 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Mar 10 06:22 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Mar 10 06:22 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 17M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 10 06:16 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 10 06:15 .. -rw-r--r-- 1 kkarri waxmanlab 336 Mar 10 06:16 DiffExp_5g_Venn_Tables_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.7M Mar 10 06:16 DiffExp_v2_LncRNA_Intronic_Only_M2WTM_M2Ezh12M_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 15K Mar 10 06:16 Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 21K Mar 10 06:16 Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.2M Mar 10 06:16 M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.4M Mar 10 06:16 M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 931K Mar 10 06:16 M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M Mar 10 06:16 M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.9K Mar 10 06:16 Up_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.1K Mar 10 06:16 Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 43K Mar 10 06:16 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 41K Mar 10 06:16 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Tue Mar 10 06:23:49 EDT 2020 0 minutes and 58 seconds elapsed. ==========================================================