----------------------- 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_16_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_2M CONDITION_2_NAME: Ezh12F_2M 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_16e COL_SUFFIX: LncRNA_GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 17 10:29:03 EDT 2020 Running on node : scc-tm4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_16_lncRNA_featureCounts Current job ID : 3911221 Current job name : Step_08c_DiffExp_16e Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3911221.1.linga Loading required modules... ------------------------------------------ Sample_DIR: M2Ezh12M_1 Sample_ID: M2Ezh12M_1 Description: M2Ezh12M_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: M2Ezh12M_2 Sample_ID: M2Ezh12M_2 Description: M2Ezh12M_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 Sample_DIR: M2Ezh12M_3 Sample_ID: M2Ezh12M_3 Description: M2Ezh12M_3 M_Num: 3 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: 123 ------------------------------------------ ------------------------------------------ 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: 3 NUM_REP_CONDITION1: 3 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status M2Ezh12F_1_sorted.bam Assigned 24762427 Unassigned_Ambiguity 6427864 Unassigned_MultiMapping 0 Unassigned_NoFeatures 6457722 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 12294742 Unassigned_Ambiguity 3588158 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2670780 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 10465276 Unassigned_Ambiguity 3135512 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2717023 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 718718 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M0.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M0.summary -rw-r--r-- 1 kkarri waxmanlab 713862 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M1.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M1.summary -rw-r--r-- 1 kkarri waxmanlab 711787 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M2.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M2.summary -rw-r--r-- 1 kkarri waxmanlab 715408 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12M_2M0.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12M_2M0.summary -rw-r--r-- 1 kkarri waxmanlab 712971 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12M_2M1.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12M_2M1.summary -rw-r--r-- 1 kkarri waxmanlab 709535 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12M_2M2.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12M_2M2.summary -rw-r--r-- 1 kkarri waxmanlab 815529 Mar 17 10:29 /scratch/3911221.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/3911221.1.linga/Input/Ezh12F_2M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 17 10:29 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 17 10:29 .. /scratch/3911221.1.linga/Input/Ezh12M_2M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 17 10:29 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 17 10:29 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Ezh12M_2M Ezh12F_2M 3 3 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/3911221.1.linga/Input DiffExp_v2_LncRNA_GeneBody ncRNA_genebodies_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Ezh12M_2M" [1] "Ezh12F_2M" [1] 3 [1] 3 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/3911221.1.linga/Input" [1] "DiffExp_v2_LncRNA_GeneBody" [1] "ncRNA_genebodies_for_counting_lengths.txt" [1] "sum1:60329.4515949749" "sum1:51700.8908726374" "sum1:55444.8501363706" [4] "sum1:55825.0642013276" [1] "sum2:54984.9962643479" "sum2:55477.0444183601" "sum2:57209.5407081094" [4] "sum2:55890.5271302725" [1] 15558 23 [1] 15558 63 [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/3911221.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_Ezh12M_2M_Ezh12F_2M.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_GeneBody_Ezh12M_2M_Ezh12F_2M.txt Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_LncRNA_GeneBody_Ezh12M_2M_Ezh12F_2M.txt Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody ========================================================== Comparison_Info: Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_GeneBody'_'Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_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_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 4 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 13 7 [1] "Check out Up_Genes_DESeq_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt!" Rscript Diff_Genes.R Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_GeneBody'_'Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_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_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 5 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 16 7 [1] "Check out Up_Genes_EdgeR_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt Down_Genes_EdgeR_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt LncRNA_GeneBody_Counting DiffExp_16e [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_16e" [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_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt Up_Genes_EdgeR_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt LncRNA_GeneBody_Counting DiffExp_16e [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_16e" [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: Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 302 Mar 17 10:29 /scratch/3911221.1.linga/Input/DiffExp_16e_Venn_Tables_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 5390642 Mar 17 10:29 /scratch/3911221.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_Ezh12M_2M_Ezh12F_2M.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Mar 17 10:29 /scratch/3911221.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 1365 Mar 17 10:29 /scratch/3911221.1.linga/Input/Down_Genes_DESeq_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 1779 Mar 17 10:29 /scratch/3911221.1.linga/Input/Down_Genes_EdgeR_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 718718 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M0.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M0.summary -rw-r--r-- 1 kkarri waxmanlab 713862 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M1.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M1.summary -rw-r--r-- 1 kkarri waxmanlab 711787 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M2.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M2.summary -rw-r--r-- 1 kkarri waxmanlab 1919141 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2059163 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 963786 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1345288 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 715408 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12M_2M0.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12M_2M0.summary -rw-r--r-- 1 kkarri waxmanlab 712971 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12M_2M1.out -rw-r--r-- 1 kkarri waxmanlab 302 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12M_2M1.summary -rw-r--r-- 1 kkarri waxmanlab 709535 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12M_2M2.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 17 10:29 /scratch/3911221.1.linga/Input/Ezh12M_2M2.summary -rw-r--r-- 1 kkarri waxmanlab 519 Mar 17 10:29 /scratch/3911221.1.linga/Input/Up_Genes_DESeq_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 655 Mar 17 10:29 /scratch/3911221.1.linga/Input/Up_Genes_EdgeR_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Mar 17 10:29 /scratch/3911221.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 43865 Mar 17 10:29 /scratch/3911221.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 41908 Mar 17 10:29 /scratch/3911221.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 4968 Mar 17 10:29 /scratch/3911221.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Mar 17 10:29 /scratch/3911221.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 815529 Mar 17 10:29 /scratch/3911221.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/3911221.1.linga/Input/Ezh12F_2M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 17 10:29 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 17 10:29 .. /scratch/3911221.1.linga/Input/Ezh12M_2M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 17 10:29 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 17 10:29 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Mar 17 10:29 . drwxrwxrwt. 11 root root 4.0K Mar 17 10:28 .. -rw-r--r-- 1 kkarri waxmanlab 132 Mar 17 10:29 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 132 Mar 17 10:29 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 17 10:29 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Mar 17 10:29 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Mar 17 10:29 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 26M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 17 10:22 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 17 10:21 .. -rw-r--r-- 1 kkarri waxmanlab 302 Mar 17 10:22 DiffExp_16e_Venn_Tables_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.2M Mar 17 10:22 DiffExp_v2_LncRNA_GeneBody_Ezh12M_2M_Ezh12F_2M_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.4K Mar 17 10:22 Down_Genes_DESeq_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.8K Mar 17 10:22 Down_Genes_EdgeR_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.9M Mar 17 10:22 Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.0M Mar 17 10:22 Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 942K Mar 17 10:22 Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.3M Mar 17 10:22 Ezh12F_2M_GSE118757_123_vs_Ezh12M_2M_GSE118757_123_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 519 Mar 17 10:22 Up_Genes_DESeq_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 655 Mar 17 10:22 Up_Genes_EdgeR_LncRNA_GeneBody_Ezh12F_2M_GSE118757_123_Ezh12M_2M_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 43K Mar 17 10:22 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 41K Mar 17 10:22 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Tue Mar 17 10:29:49 EDT 2020 0 minutes and 46 seconds elapsed. ==========================================================