----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/09c_DiffExp_1_lncRNA_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV Dataset_Label: G166_Env ANNOTATION_FILE_DIR: /restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files ANNOTATION_FILE: /restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files/ncRNA_output_filtered_final_gene.txt CONDITION_1_NAME: M_control CONDITION_2_NAME: M_TCPO_1d Lengths_DIR: /restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/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_1g COL_SUFFIX: LncRNA_Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed Apr 24 19:02:07 EDT 2019 Running on node : scc-ka8 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/09c_DiffExp_1_lncRNA_featureCounts Current job ID : 5561366 Current job name : Step_09c_DiffExp_1g Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5561366.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G166_M1 Sample_ID: G166_M1 Description: M1_control M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G166_M2 Sample_ID: G166_M2 Description: M2_control M_Num: M2 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: M1M2 ------------------------------------------ ------------------------------------------ Sample_DIR: G166_M4 Sample_ID: G166_M4 Description: Male_TCPOBOP_1d M_Num: M4 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G166_M5 Sample_ID: G166_M5 Description: Male_TCPOBOP_1d M_Num: M5 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G166_M6 Sample_ID: G166_M6 Description: Male_TCPOBOP_1d M_Num: M6 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: M4M5M6 ------------------------------------------ ========================================================== 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 G166_M4_sorted.bam Assigned 7522734 Unassigned_Ambiguity 287632 Unassigned_MultiMapping 0 Unassigned_NoFeatures 5279848 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G166_M5_sorted.bam Assigned 8281740 Unassigned_Ambiguity 252333 Unassigned_MultiMapping 0 Unassigned_NoFeatures 12850062 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G166_M6_sorted.bam Assigned 405166 Unassigned_Ambiguity 12084 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1669752 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G166_M1_sorted.bam Assigned 2494232 Unassigned_Ambiguity 68254 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2981251 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G166_M2_sorted.bam Assigned 11719041 Unassigned_Ambiguity 296345 Unassigned_MultiMapping 0 Unassigned_NoFeatures 18197913 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 353580 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_TCPO_1d0.out -rw-r--r-- 1 kkarri waxmanlab 297 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_TCPO_1d0.summary -rw-r--r-- 1 kkarri waxmanlab 356563 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_TCPO_1d1.out -rw-r--r-- 1 kkarri waxmanlab 298 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_TCPO_1d1.summary -rw-r--r-- 1 kkarri waxmanlab 342209 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_TCPO_1d2.out -rw-r--r-- 1 kkarri waxmanlab 295 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_TCPO_1d2.summary -rw-r--r-- 1 kkarri waxmanlab 349644 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_control0.out -rw-r--r-- 1 kkarri waxmanlab 296 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_control0.summary -rw-r--r-- 1 kkarri waxmanlab 359031 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_control1.out -rw-r--r-- 1 kkarri waxmanlab 299 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_control1.summary -rw-r--r-- 1 kkarri waxmanlab 414633 Apr 24 19:02 /scratch/5561366.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/5561366.1.linga/Input/M_TCPO_1d: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 24 19:02 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 24 19:02 .. /scratch/5561366.1.linga/Input/M_control: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 24 19:02 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 24 19:02 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R M_control M_TCPO_1d 2 3 /restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/5561366.1.linga/Input DiffExp_v2_LncRNA_Intronic_Only intronic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "M_control" [1] "M_TCPO_1d" [1] 2 [1] 3 [1] "/restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/5561366.1.linga/Input" [1] "DiffExp_v2_LncRNA_Intronic_Only" [1] "intronic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] 15572 23 [1] 15572 53 [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/5561366.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_M_control_M_TCPO_1d.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Intronic_Only_M_control_M_TCPO_1d.txt M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_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_M_control_M_TCPO_1d.txt M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload 1 LncRNA_Intronic_Only ========================================================== Comparison_Info: M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Intronic_Only'_'M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_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_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 7 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 1 7 [1] "Check out Up_Genes_DESeq_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt!" Rscript Diff_Genes.R M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Intronic_Only'_'M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_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_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 2 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 1 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt Down_Genes_EdgeR_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt LncRNA_Intronic_Only_Counting DiffExp_1g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1g" [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_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt Up_Genes_EdgeR_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt LncRNA_Intronic_Only_Counting DiffExp_1g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1g" [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: M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 328 Apr 24 19:03 /scratch/5561366.1.linga/Input/DiffExp_1g_Venn_Tables_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 3585130 Apr 24 19:03 /scratch/5561366.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_M_control_M_TCPO_1d.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Apr 24 19:02 /scratch/5561366.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 295 Apr 24 19:03 /scratch/5561366.1.linga/Input/Down_Genes_DESeq_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 293 Apr 24 19:03 /scratch/5561366.1.linga/Input/Down_Genes_EdgeR_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 353580 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_TCPO_1d0.out -rw-r--r-- 1 kkarri waxmanlab 297 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_TCPO_1d0.summary -rw-r--r-- 1 kkarri waxmanlab 356563 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_TCPO_1d1.out -rw-r--r-- 1 kkarri waxmanlab 298 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_TCPO_1d1.summary -rw-r--r-- 1 kkarri waxmanlab 342209 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_TCPO_1d2.out -rw-r--r-- 1 kkarri waxmanlab 295 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_TCPO_1d2.summary -rw-r--r-- 1 kkarri waxmanlab 2201046 Apr 24 19:03 /scratch/5561366.1.linga/Input/M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1874034 Apr 24 19:03 /scratch/5561366.1.linga/Input/M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1687088 Apr 24 19:03 /scratch/5561366.1.linga/Input/M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1360076 Apr 24 19:03 /scratch/5561366.1.linga/Input/M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 349644 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_control0.out -rw-r--r-- 1 kkarri waxmanlab 296 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_control0.summary -rw-r--r-- 1 kkarri waxmanlab 359031 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_control1.out -rw-r--r-- 1 kkarri waxmanlab 299 Apr 24 19:02 /scratch/5561366.1.linga/Input/M_control1.summary -rw-r--r-- 1 kkarri waxmanlab 999 Apr 24 19:03 /scratch/5561366.1.linga/Input/Up_Genes_DESeq_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 386 Apr 24 19:03 /scratch/5561366.1.linga/Input/Up_Genes_EdgeR_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Apr 24 19:02 /scratch/5561366.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 31783 Apr 24 19:03 /scratch/5561366.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 37023 Apr 24 19:03 /scratch/5561366.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 4968 Apr 24 19:02 /scratch/5561366.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Apr 24 19:02 /scratch/5561366.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 414633 Apr 24 19:02 /scratch/5561366.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/5561366.1.linga/Input/M_TCPO_1d: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 24 19:02 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 24 19:03 .. /scratch/5561366.1.linga/Input/M_control: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 24 19:02 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 24 19:03 .. ========================================================== List files in scratch total 3.0M drwx------ 3 kkarri waxmanlab 4.0K Apr 24 19:03 . drwxrwxrwt. 66 root root 72K Apr 24 19:02 .. -rw-r--r-- 1 kkarri waxmanlab 87 Apr 24 19:02 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 129 Apr 24 19:02 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Apr 24 19:03 Input -rwxr-xr-x 1 kkarri waxmanlab 14K Apr 24 19:02 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 2.9M Apr 24 19:02 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 20M drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 24 18:57 . drwxr-xr-x 8 kkarri waxmanlab 4.0K Apr 24 18:56 .. -rw-r--r-- 1 kkarri waxmanlab 328 Apr 24 18:57 DiffExp_1g_Venn_Tables_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.5M Apr 24 18:57 DiffExp_v2_LncRNA_Intronic_Only_M_control_M_TCPO_1d_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 295 Apr 24 18:57 Down_Genes_DESeq_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 293 Apr 24 18:57 Down_Genes_EdgeR_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.1M Apr 24 18:57 M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.8M Apr 24 18:57 M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.7M Apr 24 18:57 M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.3M Apr 24 18:57 M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 999 Apr 24 18:57 Up_Genes_DESeq_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 386 Apr 24 18:57 Up_Genes_EdgeR_LncRNA_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 32K Apr 24 18:57 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 37K Apr 24 18:57 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Wed Apr 24 19:03:17 EDT 2019 1 minutes and 10 seconds elapsed. ==========================================================