----------------------- 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_13_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: WTM_P14 CONDITION_2_NAME: WTF_P14 Lengths_DIR: /unprotected/projects/waxmanlab/routines/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_13g COL_SUFFIX: LncRNA_Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 17 10:26:15 EDT 2020 Running on node : scc-tm1 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_13_lncRNA_featureCounts Current job ID : 3911197 Current job name : Step_08c_DiffExp_13g Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3911197.1.linga Loading required modules... ------------------------------------------ Sample_DIR: WTM_1 Sample_ID: WTM_1 Description: WTM_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: WTM_2 Sample_ID: WTM_2 Description: WTM_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: WTM_3 Sample_ID: WTM_3 Description: WTM_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: WTF_1 Sample_ID: WTF_1 Description: WTF_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: WTF_2 Sample_ID: WTF_2 Description: WTF_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 M_Num_Cond2_List: 12 ------------------------------------------ ========================================================== 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 WTF_1_sorted.bam Assigned 2998711 Unassigned_Ambiguity 526122 Unassigned_MultiMapping 0 Unassigned_NoFeatures 14856921 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status WTF_2_sorted.bam Assigned 2692992 Unassigned_Ambiguity 522013 Unassigned_MultiMapping 0 Unassigned_NoFeatures 13761930 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status WTM_1_sorted.bam Assigned 1767633 Unassigned_Ambiguity 380002 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11204170 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status WTM_2_sorted.bam Assigned 1643568 Unassigned_Ambiguity 427456 Unassigned_MultiMapping 0 Unassigned_NoFeatures 13326780 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status WTM_3_sorted.bam Assigned 2868412 Unassigned_Ambiguity 481525 Unassigned_MultiMapping 0 Unassigned_NoFeatures 13065939 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 349260 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTF_P140.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTF_P140.summary -rw-r--r-- 1 kkarri waxmanlab 348932 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTF_P141.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTF_P141.summary -rw-r--r-- 1 kkarri waxmanlab 346103 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTM_P140.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTM_P140.summary -rw-r--r-- 1 kkarri waxmanlab 344789 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTM_P141.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTM_P141.summary -rw-r--r-- 1 kkarri waxmanlab 349686 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTM_P142.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTM_P142.summary -rw-r--r-- 1 kkarri waxmanlab 414633 Mar 17 10:26 /scratch/3911197.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3911197.1.linga/Input/WTF_P14: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 17 10:26 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 17 10:26 .. /scratch/3911197.1.linga/Input/WTM_P14: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 17 10:26 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 17 10:26 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WTM_P14 WTF_P14 3 2 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/3911197.1.linga/Input DiffExp_v2_LncRNA_Intronic_Only intronic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WTM_P14" [1] "WTF_P14" [1] 3 [1] 2 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/3911197.1.linga/Input" [1] "DiffExp_v2_LncRNA_Intronic_Only" [1] "intronic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] "sum1:25578.3688596267" "sum1:24736.0558100814" "sum1:27847.1602626022" [4] "sum1:26053.8616441034" [1] "sum2:30246.0075730227" "sum2:32515.1154566466" "sum2:31380.5615148346" [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/3911197.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_WTM_P14_WTF_P14.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Intronic_Only_WTM_P14_WTF_P14.txt WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_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_WTM_P14_WTF_P14.txt WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload 1 LncRNA_Intronic_Only ========================================================== Comparison_Info: WTF_P14_GSE118757_12_WTM_P14_GSE118757_123 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Intronic_Only'_'WTF_P14_GSE118757_12_WTM_P14_GSE118757_123 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_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_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 0 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_DESeq_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt!" Rscript Diff_Genes.R WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Intronic_Only'_'WTF_P14_GSE118757_12_WTM_P14_GSE118757_123 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_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_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 1 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 2 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt Down_Genes_EdgeR_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt LncRNA_Intronic_Only_Counting DiffExp_13g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_13g" [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_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt Up_Genes_EdgeR_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt LncRNA_Intronic_Only_Counting DiffExp_13g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_13g" [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: WTF_P14_GSE118757_12_WTM_P14_GSE118757_123 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 330 Mar 17 10:27 /scratch/3911197.1.linga/Input/DiffExp_13g_Venn_Tables_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 3894560 Mar 17 10:26 /scratch/3911197.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_WTM_P14_WTF_P14.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Mar 17 10:26 /scratch/3911197.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 223 Mar 17 10:26 /scratch/3911197.1.linga/Input/Down_Genes_DESeq_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 362 Mar 17 10:26 /scratch/3911197.1.linga/Input/Down_Genes_EdgeR_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 223 Mar 17 10:26 /scratch/3911197.1.linga/Input/Up_Genes_DESeq_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 287 Mar 17 10:26 /scratch/3911197.1.linga/Input/Up_Genes_EdgeR_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Mar 17 10:26 /scratch/3911197.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 33754 Mar 17 10:27 /scratch/3911197.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 32467 Mar 17 10:27 /scratch/3911197.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 349260 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTF_P140.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTF_P140.summary -rw-r--r-- 1 kkarri waxmanlab 348932 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTF_P141.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTF_P141.summary -rw-r--r-- 1 kkarri waxmanlab 1592454 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1654686 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 641602 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 821699 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 346103 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTM_P140.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTM_P140.summary -rw-r--r-- 1 kkarri waxmanlab 344789 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTM_P141.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTM_P141.summary -rw-r--r-- 1 kkarri waxmanlab 349686 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTM_P142.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 17 10:26 /scratch/3911197.1.linga/Input/WTM_P142.summary -rwxr-xr-x 1 kkarri waxmanlab 4968 Mar 17 10:26 /scratch/3911197.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Mar 17 10:26 /scratch/3911197.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 414633 Mar 17 10:26 /scratch/3911197.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3911197.1.linga/Input/WTF_P14: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 17 10:26 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 17 10:27 .. /scratch/3911197.1.linga/Input/WTM_P14: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 17 10:26 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 17 10:27 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Mar 17 10:27 . drwxrwxrwt. 14 root root 4.0K Mar 17 10:26 .. -rw-r--r-- 1 kkarri waxmanlab 87 Mar 17 10:26 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 69 Mar 17 10:26 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 17 10:27 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Mar 17 10:26 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Mar 17 10:26 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 13M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 17 10:19 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 17 10:18 .. -rw-r--r-- 1 kkarri waxmanlab 330 Mar 17 10:19 DiffExp_13g_Venn_Tables_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.8M Mar 17 10:19 DiffExp_v2_LncRNA_Intronic_Only_WTM_P14_WTF_P14_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 223 Mar 17 10:19 Down_Genes_DESeq_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 362 Mar 17 10:19 Down_Genes_EdgeR_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 223 Mar 17 10:19 Up_Genes_DESeq_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 287 Mar 17 10:19 Up_Genes_EdgeR_LncRNA_Intronic_Only_WTF_P14_GSE118757_12_WTM_P14_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 33K Mar 17 10:19 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 32K Mar 17 10:19 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 1.6M Mar 17 10:19 WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M Mar 17 10:19 WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 627K Mar 17 10:19 WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 803K Mar 17 10:19 WTF_P14_GSE118757_12_vs_WTM_P14_GSE118757_123_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt ========================================================== ========================================================== Finished on : Tue Mar 17 10:27:05 EDT 2020 0 minutes and 50 seconds elapsed. ==========================================================