----------------------- 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_10_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: Ezh12M CONDITION_2_NAME: M2Ezh12M 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_10f COL_SUFFIX: LncRNA_Exonic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 10 14:06:43 EDT 2020 Running on node : scc-ka4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_10_lncRNA_featureCounts Current job ID : 3784424 Current job name : Step_08c_DiffExp_10f Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3784424.1.linga Loading required modules... ------------------------------------------ Sample_DIR: Ezh12M_1 Sample_ID: Ezh12M_1 Description: Ezh12M_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: Ezh12M_2 Sample_ID: Ezh12M_2 Description: Ezh12M_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 Ezh12M_1_sorted.bam Assigned 3996540 Unassigned_Ambiguity 783405 Unassigned_MultiMapping 0 Unassigned_NoFeatures 8709470 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12M_2_sorted.bam Assigned 6006885 Unassigned_Ambiguity 1314530 Unassigned_MultiMapping 0 Unassigned_NoFeatures 4906550 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2Ezh12M_1_sorted.bam Assigned 5334169 Unassigned_Ambiguity 931659 Unassigned_MultiMapping 0 Unassigned_NoFeatures 4722513 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 4827372 Unassigned_Ambiguity 849837 Unassigned_MultiMapping 0 Unassigned_NoFeatures 5596158 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 2845421 Unassigned_Ambiguity 506809 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2849636 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 706950 Mar 10 14:06 /scratch/3784424.1.linga/Input/Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 14:06 /scratch/3784424.1.linga/Input/Ezh12M0.summary -rw-r--r-- 1 kkarri waxmanlab 709181 Mar 10 14:06 /scratch/3784424.1.linga/Input/Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 14:06 /scratch/3784424.1.linga/Input/Ezh12M1.summary -rw-r--r-- 1 kkarri waxmanlab 710792 Mar 10 14:06 /scratch/3784424.1.linga/Input/M2Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 14:06 /scratch/3784424.1.linga/Input/M2Ezh12M0.summary -rw-r--r-- 1 kkarri waxmanlab 708550 Mar 10 14:06 /scratch/3784424.1.linga/Input/M2Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 14:06 /scratch/3784424.1.linga/Input/M2Ezh12M1.summary -rw-r--r-- 1 kkarri waxmanlab 705968 Mar 10 14:06 /scratch/3784424.1.linga/Input/M2Ezh12M2.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 14:06 /scratch/3784424.1.linga/Input/M2Ezh12M2.summary -rw-r--r-- 1 kkarri waxmanlab 794757 Mar 10 14:06 /scratch/3784424.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3784424.1.linga/Input/Ezh12M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:06 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:06 .. /scratch/3784424.1.linga/Input/M2Ezh12M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:06 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:06 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Ezh12M M2Ezh12M 2 3 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/3784424.1.linga/Input DiffExp_v2_LncRNA_Exonic_Only exonic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Ezh12M" [1] "M2Ezh12M" [1] 2 [1] 3 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/3784424.1.linga/Input" [1] "DiffExp_v2_LncRNA_Exonic_Only" [1] "exonic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] "sum1:124163.166348685" "sum1:218516.761472521" "sum1:171339.963910603" [1] "sum2:194324.574038991" "sum2:167551.268839335" "sum2:183187.518045443" [4] "sum2:181687.78697459" [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/3784424.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_Ezh12M_M2Ezh12M.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Exonic_Only_Ezh12M_M2Ezh12M.txt M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_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_Ezh12M_M2Ezh12M.txt M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only ========================================================== Comparison_Info: M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Exonic_Only'_'M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_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_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 38 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 22 7 [1] "Check out Up_Genes_DESeq_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt!" Rscript Diff_Genes.R M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Exonic_Only'_'M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_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_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 38 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 21 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt Down_Genes_EdgeR_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt LncRNA_Exonic_Only_Counting DiffExp_10f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_10f" [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_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt Up_Genes_EdgeR_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt LncRNA_Exonic_Only_Counting DiffExp_10f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_10f" [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: M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 322 Mar 10 14:07 /scratch/3784424.1.linga/Input/DiffExp_10f_Venn_Tables_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 5044665 Mar 10 14:07 /scratch/3784424.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_Ezh12M_M2Ezh12M.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Mar 10 14:06 /scratch/3784424.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 5927 Mar 10 14:07 /scratch/3784424.1.linga/Input/Down_Genes_DESeq_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 3681 Mar 10 14:07 /scratch/3784424.1.linga/Input/Down_Genes_EdgeR_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 706950 Mar 10 14:06 /scratch/3784424.1.linga/Input/Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 14:06 /scratch/3784424.1.linga/Input/Ezh12M0.summary -rw-r--r-- 1 kkarri waxmanlab 709181 Mar 10 14:06 /scratch/3784424.1.linga/Input/Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 14:06 /scratch/3784424.1.linga/Input/Ezh12M1.summary -rw-r--r-- 1 kkarri waxmanlab 710792 Mar 10 14:06 /scratch/3784424.1.linga/Input/M2Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 14:06 /scratch/3784424.1.linga/Input/M2Ezh12M0.summary -rw-r--r-- 1 kkarri waxmanlab 708550 Mar 10 14:06 /scratch/3784424.1.linga/Input/M2Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 14:06 /scratch/3784424.1.linga/Input/M2Ezh12M1.summary -rw-r--r-- 1 kkarri waxmanlab 705968 Mar 10 14:06 /scratch/3784424.1.linga/Input/M2Ezh12M2.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 14:06 /scratch/3784424.1.linga/Input/M2Ezh12M2.summary -rw-r--r-- 1 kkarri waxmanlab 4486228 Mar 10 14:07 /scratch/3784424.1.linga/Input/M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 3023776 Mar 10 14:07 /scratch/3784424.1.linga/Input/M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 2267347 Mar 10 14:07 /scratch/3784424.1.linga/Input/M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2322368 Mar 10 14:07 /scratch/3784424.1.linga/Input/M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 3799 Mar 10 14:07 /scratch/3784424.1.linga/Input/Up_Genes_DESeq_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 3654 Mar 10 14:07 /scratch/3784424.1.linga/Input/Up_Genes_EdgeR_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Mar 10 14:06 /scratch/3784424.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 44948 Mar 10 14:07 /scratch/3784424.1.linga/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 42832 Mar 10 14:07 /scratch/3784424.1.linga/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 794757 Mar 10 14:06 /scratch/3784424.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt -rwxr-xr-x 1 kkarri waxmanlab 4968 Mar 10 14:06 /scratch/3784424.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Mar 10 14:06 /scratch/3784424.1.linga/Input/formatForSegex_ver4.R /scratch/3784424.1.linga/Input/Ezh12M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:06 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:07 .. /scratch/3784424.1.linga/Input/M2Ezh12M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:06 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:07 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Mar 10 14:07 . drwxrwxrwt. 32 root root 4.0K Mar 10 14:06 .. -rw-r--r-- 1 kkarri waxmanlab 87 Mar 10 14:06 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 132 Mar 10 14:06 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 10 14:07 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Mar 10 14:06 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Mar 10 14:06 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 38M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 10 14:00 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 10 13:59 .. -rw-r--r-- 1 kkarri waxmanlab 322 Mar 10 14:00 DiffExp_10f_Venn_Tables_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.9M Mar 10 14:00 DiffExp_v2_LncRNA_Exonic_Only_Ezh12M_M2Ezh12M_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.8K Mar 10 14:00 Down_Genes_DESeq_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.6K Mar 10 14:00 Down_Genes_EdgeR_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.3M Mar 10 14:00 M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.9M Mar 10 14:00 M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.2M Mar 10 14:00 M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Mar 10 14:00 M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.8K Mar 10 14:00 Up_Genes_DESeq_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.6K Mar 10 14:00 Up_Genes_EdgeR_LncRNA_Exonic_Only_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 44K Mar 10 14:00 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 42K Mar 10 14:00 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Tue Mar 10 14:07:54 EDT 2020 1 minutes and 11 seconds elapsed. ==========================================================