----------------------- 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: ncRNA_genebodies_for_counting_lengths.txt COUNT_DIR: LncRNA_GeneBody_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_GeneBody DiffExp_Index: DiffExp_10e COL_SUFFIX: LncRNA_GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 10 14:06:43 EDT 2020 Running on node : scc-tm2 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_10_lncRNA_featureCounts Current job ID : 3784423 Current job name : Step_08c_DiffExp_10e Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3784423.1.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 11437280 Unassigned_Ambiguity 2757099 Unassigned_MultiMapping 0 Unassigned_NoFeatures 4182464 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 12688148 Unassigned_Ambiguity 4175077 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2100717 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 12231289 Unassigned_Ambiguity 3323511 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1966599 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 10839710 Unassigned_Ambiguity 3288364 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3251350 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 5997010 Unassigned_Ambiguity 1725312 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1460211 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 711221 Mar 10 14:06 /scratch/3784423.1.linga/Input/Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 14:06 /scratch/3784423.1.linga/Input/Ezh12M0.summary -rw-r--r-- 1 kkarri waxmanlab 712735 Mar 10 14:06 /scratch/3784423.1.linga/Input/Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 14:06 /scratch/3784423.1.linga/Input/Ezh12M1.summary -rw-r--r-- 1 kkarri waxmanlab 715408 Mar 10 14:06 /scratch/3784423.1.linga/Input/M2Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 10 14:06 /scratch/3784423.1.linga/Input/M2Ezh12M0.summary -rw-r--r-- 1 kkarri waxmanlab 712971 Mar 10 14:06 /scratch/3784423.1.linga/Input/M2Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 10 14:06 /scratch/3784423.1.linga/Input/M2Ezh12M1.summary -rw-r--r-- 1 kkarri waxmanlab 709535 Mar 10 14:06 /scratch/3784423.1.linga/Input/M2Ezh12M2.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 14:06 /scratch/3784423.1.linga/Input/M2Ezh12M2.summary -rw-r--r-- 1 kkarri waxmanlab 815529 Mar 10 14:06 /scratch/3784423.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/3784423.1.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/3784423.1.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/3784423.1.linga/Input DiffExp_v2_LncRNA_GeneBody ncRNA_genebodies_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/3784423.1.linga/Input" [1] "DiffExp_v2_LncRNA_GeneBody" [1] "ncRNA_genebodies_for_counting_lengths.txt" [1] "sum1:72489.8974071849" "sum1:68246.0705060296" "sum1:70367.9839566073" [1] "sum2:60329.4515949749" "sum2:51700.8908726374" "sum2:55444.8501363706" [4] "sum2:55825.0642013276" [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/3784423.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_Ezh12M_M2Ezh12M.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_GeneBody_Ezh12M_M2Ezh12M.txt M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_LncRNA_GeneBody_Ezh12M_M2Ezh12M.txt M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody ========================================================== 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_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_GeneBody'_'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_GeneBody_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 36 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 19 7 [1] "Check out Up_Genes_DESeq_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt!" Rscript Diff_Genes.R M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_GeneBody'_'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_GeneBody_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 42 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 24 7 [1] "Check out Up_Genes_EdgeR_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt Down_Genes_EdgeR_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt LncRNA_GeneBody_Counting DiffExp_10e [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_10e" [1] "-----------------" [1] "Down.DESeq.GeneBody.HTSeq" [1] "Down.EdgeR.GeneBody.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_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt Up_Genes_EdgeR_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt LncRNA_GeneBody_Counting DiffExp_10e [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_10e" [1] "-----------------" [1] "Up.DESeq.GeneBody.HTSeq" [1] "Up.EdgeR.GeneBody.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 305 Mar 10 14:07 /scratch/3784423.1.linga/Input/DiffExp_10e_Venn_Tables_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 5398524 Mar 10 14:07 /scratch/3784423.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_Ezh12M_M2Ezh12M.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Mar 10 14:06 /scratch/3784423.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 5628 Mar 10 14:07 /scratch/3784423.1.linga/Input/Down_Genes_DESeq_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 4779 Mar 10 14:07 /scratch/3784423.1.linga/Input/Down_Genes_EdgeR_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 711221 Mar 10 14:06 /scratch/3784423.1.linga/Input/Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 14:06 /scratch/3784423.1.linga/Input/Ezh12M0.summary -rw-r--r-- 1 kkarri waxmanlab 712735 Mar 10 14:06 /scratch/3784423.1.linga/Input/Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 14:06 /scratch/3784423.1.linga/Input/Ezh12M1.summary -rw-r--r-- 1 kkarri waxmanlab 715408 Mar 10 14:06 /scratch/3784423.1.linga/Input/M2Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 10 14:06 /scratch/3784423.1.linga/Input/M2Ezh12M0.summary -rw-r--r-- 1 kkarri waxmanlab 712971 Mar 10 14:06 /scratch/3784423.1.linga/Input/M2Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 10 14:06 /scratch/3784423.1.linga/Input/M2Ezh12M1.summary -rw-r--r-- 1 kkarri waxmanlab 709535 Mar 10 14:06 /scratch/3784423.1.linga/Input/M2Ezh12M2.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 14:06 /scratch/3784423.1.linga/Input/M2Ezh12M2.summary -rw-r--r-- 1 kkarri waxmanlab 4828483 Mar 10 14:07 /scratch/3784423.1.linga/Input/M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 3366031 Mar 10 14:07 /scratch/3784423.1.linga/Input/M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 2376456 Mar 10 14:07 /scratch/3784423.1.linga/Input/M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2725309 Mar 10 14:07 /scratch/3784423.1.linga/Input/M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 3629 Mar 10 14:07 /scratch/3784423.1.linga/Input/Up_Genes_DESeq_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 4154 Mar 10 14:07 /scratch/3784423.1.linga/Input/Up_Genes_EdgeR_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Mar 10 14:06 /scratch/3784423.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 43802 Mar 10 14:07 /scratch/3784423.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 42500 Mar 10 14:07 /scratch/3784423.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 4968 Mar 10 14:06 /scratch/3784423.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Mar 10 14:06 /scratch/3784423.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 815529 Mar 10 14:06 /scratch/3784423.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/3784423.1.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/3784423.1.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. 11 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 39M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 10 13:59 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 10 13:59 .. -rw-r--r-- 1 kkarri waxmanlab 305 Mar 10 13:59 DiffExp_10e_Venn_Tables_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.2M Mar 10 13:59 DiffExp_v2_LncRNA_GeneBody_Ezh12M_M2Ezh12M_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.5K Mar 10 13:59 Down_Genes_DESeq_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.7K Mar 10 13:59 Down_Genes_EdgeR_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.7M Mar 10 13:59 M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.3M Mar 10 13:59 M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Mar 10 13:59 M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.6M Mar 10 13:59 M2Ezh12M_GSE118757_123_vs_Ezh12M_GSE118757_12_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.6K Mar 10 13:59 Up_Genes_DESeq_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.1K Mar 10 13:59 Up_Genes_EdgeR_LncRNA_GeneBody_M2Ezh12M_GSE118757_123_Ezh12M_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 43K Mar 10 13:59 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 42K Mar 10 13:59 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Tue Mar 10 14:07:25 EDT 2020 0 minutes and 42 seconds elapsed. 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