----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09c_DiffExp_3_lncRNA_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP Dataset_Label: G168_TCPO_Env 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: WT_TCPO_D2 CONDITION_2_NAME: MetEGFKO_TCPO_D2 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_3f COL_SUFFIX: LncRNA_Exonic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon May 6 13:38:18 EDT 2019 Running on node : scc-kb1 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09c_DiffExp_3_lncRNA_featureCounts Current job ID : 5891734 Current job name : Step_09c_DiffExp_3f Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5891734.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G168_G169_M12 Sample_ID: G168_G169_M12 Description: WT1_TCPO_D2 M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G168_G169_M13 Sample_ID: G168_G169_M13 Description: WT2_TCPO_D2 M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G168_G169_M14 Sample_ID: G168_G169_M14 Description: WT3_TCPO_D2 M_Num: G169 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: G169G169G169 ------------------------------------------ ------------------------------------------ Sample_DIR: G168_G169_M15 Sample_ID: G168_G169_M15 Description: Met_EGFKO1_TCPO_D2 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G168_G169_M16 Sample_ID: G168_G169_M16 Description: Met_EGFKO2_TCPO_D2 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G168_G169_M17 Sample_ID: G168_G169_M17 Description: Met_EGFKO3_TCPO_D2 M_Num: G169 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: G169G169G169 ------------------------------------------ ========================================================== 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 G168_G169_M15_sorted.bam Assigned 8686312 Unassigned_Ambiguity 9703 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2789479 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M16_sorted.bam Assigned 8889004 Unassigned_Ambiguity 13279 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2802209 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M17_sorted.bam Assigned 6915975 Unassigned_Ambiguity 8937 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1986992 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M12_sorted.bam Assigned 6742140 Unassigned_Ambiguity 6352 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2402987 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M13_sorted.bam Assigned 7733326 Unassigned_Ambiguity 8494 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2703293 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M14_sorted.bam Assigned 7928181 Unassigned_Ambiguity 8116 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2783403 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 711846 May 6 13:38 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D20.out -rw-r--r-- 1 kkarri waxmanlab 301 May 6 13:38 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D20.summary -rw-r--r-- 1 kkarri waxmanlab 712067 May 6 13:38 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D21.out -rw-r--r-- 1 kkarri waxmanlab 302 May 6 13:38 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D21.summary -rw-r--r-- 1 kkarri waxmanlab 711411 May 6 13:38 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D22.out -rw-r--r-- 1 kkarri waxmanlab 301 May 6 13:38 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D22.summary -rw-r--r-- 1 kkarri waxmanlab 710341 May 6 13:38 /scratch/5891734.1.linga/Input/WT_TCPO_D20.out -rw-r--r-- 1 kkarri waxmanlab 301 May 6 13:38 /scratch/5891734.1.linga/Input/WT_TCPO_D20.summary -rw-r--r-- 1 kkarri waxmanlab 711264 May 6 13:38 /scratch/5891734.1.linga/Input/WT_TCPO_D21.out -rw-r--r-- 1 kkarri waxmanlab 301 May 6 13:38 /scratch/5891734.1.linga/Input/WT_TCPO_D21.summary -rw-r--r-- 1 kkarri waxmanlab 711529 May 6 13:38 /scratch/5891734.1.linga/Input/WT_TCPO_D22.out -rw-r--r-- 1 kkarri waxmanlab 301 May 6 13:38 /scratch/5891734.1.linga/Input/WT_TCPO_D22.summary -rw-r--r-- 1 kkarri waxmanlab 794757 May 6 13:38 /scratch/5891734.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D2: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 6 13:38 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 6 13:38 .. /scratch/5891734.1.linga/Input/WT_TCPO_D2: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 6 13:38 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 6 13:38 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WT_TCPO_D2 MetEGFKO_TCPO_D2 3 3 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/5891734.1.linga/Input DiffExp_v2_LncRNA_Exonic_Only exonic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WT_TCPO_D2" [1] "MetEGFKO_TCPO_D2" [1] 3 [1] 3 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/5891734.1.linga/Input" [1] "DiffExp_v2_LncRNA_Exonic_Only" [1] "exonic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] "sum1:284339.965741524" "sum1:286522.92927518" "sum1:287358.413799943" [4] "sum1:286073.769605549" [1] "sum2:280424.545739517" "sum2:281636.232287329" "sum2:287192.849720909" [4] "sum2:283084.542582585" [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/5891734.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_WT_TCPO_D2_MetEGFKO_TCPO_D2.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Exonic_Only_WT_TCPO_D2_MetEGFKO_TCPO_D2.txt MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_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_WT_TCPO_D2_MetEGFKO_TCPO_D2.txt MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only ========================================================== Comparison_Info: MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Exonic_Only'_'MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_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_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 47 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 58 7 [1] "Check out Up_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt!" Rscript Diff_Genes.R MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Exonic_Only'_'MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_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_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 100 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 85 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt Down_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt LncRNA_Exonic_Only_Counting DiffExp_3f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3f" [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_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt Up_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt LncRNA_Exonic_Only_Counting DiffExp_3f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3f" [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: MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 323 May 6 13:39 /scratch/5891734.1.linga/Input/DiffExp_3f_Venn_Tables_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 5982158 May 6 13:39 /scratch/5891734.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_WT_TCPO_D2_MetEGFKO_TCPO_D2.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 May 6 13:38 /scratch/5891734.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 6964 May 6 13:39 /scratch/5891734.1.linga/Input/Down_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 10451 May 6 13:39 /scratch/5891734.1.linga/Input/Down_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 711846 May 6 13:38 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D20.out -rw-r--r-- 1 kkarri waxmanlab 301 May 6 13:38 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D20.summary -rw-r--r-- 1 kkarri waxmanlab 712067 May 6 13:38 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D21.out -rw-r--r-- 1 kkarri waxmanlab 302 May 6 13:38 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D21.summary -rw-r--r-- 1 kkarri waxmanlab 711411 May 6 13:38 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D22.out -rw-r--r-- 1 kkarri waxmanlab 301 May 6 13:38 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D22.summary -rw-r--r-- 1 kkarri waxmanlab 2230330 May 6 13:39 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2261446 May 6 13:39 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1180259 May 6 13:39 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1832364 May 6 13:39 /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 4230 May 6 13:39 /scratch/5891734.1.linga/Input/Up_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 9957 May 6 13:39 /scratch/5891734.1.linga/Input/Up_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 May 6 13:38 /scratch/5891734.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 42698 May 6 13:39 /scratch/5891734.1.linga/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 38656 May 6 13:39 /scratch/5891734.1.linga/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 710341 May 6 13:38 /scratch/5891734.1.linga/Input/WT_TCPO_D20.out -rw-r--r-- 1 kkarri waxmanlab 301 May 6 13:38 /scratch/5891734.1.linga/Input/WT_TCPO_D20.summary -rw-r--r-- 1 kkarri waxmanlab 711264 May 6 13:38 /scratch/5891734.1.linga/Input/WT_TCPO_D21.out -rw-r--r-- 1 kkarri waxmanlab 301 May 6 13:38 /scratch/5891734.1.linga/Input/WT_TCPO_D21.summary -rw-r--r-- 1 kkarri waxmanlab 711529 May 6 13:38 /scratch/5891734.1.linga/Input/WT_TCPO_D22.out -rw-r--r-- 1 kkarri waxmanlab 301 May 6 13:38 /scratch/5891734.1.linga/Input/WT_TCPO_D22.summary -rw-r--r-- 1 kkarri waxmanlab 794757 May 6 13:38 /scratch/5891734.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt -rwxr-xr-x 1 kkarri waxmanlab 4968 May 6 13:38 /scratch/5891734.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 May 6 13:38 /scratch/5891734.1.linga/Input/formatForSegex_ver4.R /scratch/5891734.1.linga/Input/MetEGFKO_TCPO_D2: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 6 13:38 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 6 13:39 .. /scratch/5891734.1.linga/Input/WT_TCPO_D2: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 6 13:38 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 6 13:39 .. ========================================================== List files in scratch total 3.5M drwx------ 3 kkarri waxmanlab 4.0K May 6 13:39 . drwxrwxrwt. 39 root root 180K May 6 13:38 .. -rw-r--r-- 1 kkarri waxmanlab 153 May 6 13:38 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 174 May 6 13:38 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K May 6 13:39 Input -rwxr-xr-x 1 kkarri waxmanlab 15K May 6 13:38 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M May 6 13:38 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 29M drwxr-sr-x 2 kkarri waxmanlab 4.0K May 6 13:33 . drwxr-sr-x 7 kkarri waxmanlab 4.0K May 6 13:32 .. -rw-r--r-- 1 kkarri waxmanlab 323 May 6 13:33 DiffExp_3f_Venn_Tables_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.8M May 6 13:33 DiffExp_v2_LncRNA_Exonic_Only_WT_TCPO_D2_MetEGFKO_TCPO_D2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 6.9K May 6 13:33 Down_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 11K May 6 13:33 Down_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.2M May 6 13:33 MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.2M May 6 13:33 MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.2M May 6 13:33 MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.8M May 6 13:33 MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.2K May 6 13:33 Up_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 9.8K May 6 13:33 Up_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 42K May 6 13:33 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 38K May 6 13:33 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon May 6 13:39:33 EDT 2019 1 minutes and 15 seconds elapsed. 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