----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09c_DiffExp_2_lncRNA_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170 Dataset_Label: G170 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: F_Placebo_TD227 CONDITION_2_NAME: F_CPA_4cycle_TD227 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_2e COL_SUFFIX: LncRNA_GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Sep 16 10:44:28 EDT 2019 Running on node : scc-tm1 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09c_DiffExp_2_lncRNA_featureCounts Current job ID : 9373928 Current job name : Step_09c_DiffExp_2e Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9373928.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G170_M7 Sample_ID: G170_M7 Description: F_Placebo1_TD227 M_Num: M7 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G170_M8 Sample_ID: G170_M8 Description: F_Placebo2_TD227 M_Num: M8 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G170_M9 Sample_ID: G170_M9 Description: F_Placebo3_TD227 M_Num: M9 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: M7M8M9 ------------------------------------------ ------------------------------------------ Sample_DIR: G170_M13 Sample_ID: G170_M13 Description: F_CPA_4cycle7_TD227 M_Num: M13 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G170_M14 Sample_ID: G170_M14 Description: F_CPA_4cycle8_TD227 M_Num: M14 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G170_M15 Sample_ID: G170_M15 Description: F_CPA_4cycle9_TD227 M_Num: M15 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: M13M14M15 ------------------------------------------ ========================================================== 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 G170_M13_sorted.bam Assigned 20871057 Unassigned_Ambiguity 368487 Unassigned_MultiMapping 0 Unassigned_NoFeatures 693575 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G170_M14_sorted.bam Assigned 20644707 Unassigned_Ambiguity 335305 Unassigned_MultiMapping 0 Unassigned_NoFeatures 520507 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G170_M15_sorted.bam Assigned 23024233 Unassigned_Ambiguity 372015 Unassigned_MultiMapping 0 Unassigned_NoFeatures 677132 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G170_M7_sorted.bam Assigned 18385075 Unassigned_Ambiguity 263286 Unassigned_MultiMapping 0 Unassigned_NoFeatures 626108 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G170_M8_sorted.bam Assigned 28319695 Unassigned_Ambiguity 414702 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1564635 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G170_M9_sorted.bam Assigned 28084251 Unassigned_Ambiguity 383732 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1055425 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 723008 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD2270.out -rw-r--r-- 1 kkarri waxmanlab 298 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD2270.summary -rw-r--r-- 1 kkarri waxmanlab 722678 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD2271.out -rw-r--r-- 1 kkarri waxmanlab 298 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD2271.summary -rw-r--r-- 1 kkarri waxmanlab 723496 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD2272.out -rw-r--r-- 1 kkarri waxmanlab 298 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD2272.summary -rw-r--r-- 1 kkarri waxmanlab 721518 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_Placebo_TD2270.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_Placebo_TD2270.summary -rw-r--r-- 1 kkarri waxmanlab 726746 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_Placebo_TD2271.out -rw-r--r-- 1 kkarri waxmanlab 298 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_Placebo_TD2271.summary -rw-r--r-- 1 kkarri waxmanlab 725261 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_Placebo_TD2272.out -rw-r--r-- 1 kkarri waxmanlab 298 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_Placebo_TD2272.summary -rw-r--r-- 1 kkarri waxmanlab 815529 Sep 16 10:44 /scratch/9373928.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD227: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:44 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:44 .. /scratch/9373928.1.linga/Input/F_Placebo_TD227: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:44 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:44 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R F_Placebo_TD227 F_CPA_4cycle_TD227 3 3 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/9373928.1.linga/Input DiffExp_v2_LncRNA_GeneBody ncRNA_genebodies_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "F_Placebo_TD227" [1] "F_CPA_4cycle_TD227" [1] 3 [1] 3 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/9373928.1.linga/Input" [1] "DiffExp_v2_LncRNA_GeneBody" [1] "ncRNA_genebodies_for_counting_lengths.txt" [1] 15558 23 [1] 15558 54 [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/9373928.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_F_Placebo_TD227_F_CPA_4cycle_TD227.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_GeneBody_F_Placebo_TD227_F_CPA_4cycle_TD227.txt F_CPA_4cycle_TD227_G170_M13M14M15_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody ========================================================== Comparison_Info: F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R F_CPA_4cycle_TD227_G170_M13M14M15_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_GeneBody'_'F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_4cycle_TD227_G170_M13M14M15_vs_F_Placebo_TD227_G170_M7M8M9_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_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 27 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 36 7 [1] "Check out Up_Genes_DESeq_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt!" Rscript Diff_Genes.R F_CPA_4cycle_TD227_G170_M13M14M15_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_GeneBody'_'F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_4cycle_TD227_G170_M13M14M15_vs_F_Placebo_TD227_G170_M7M8M9_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_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 37 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 55 7 [1] "Check out Up_Genes_EdgeR_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt Down_Genes_EdgeR_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt LncRNA_GeneBody_Counting DiffExp_2e [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2e" [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_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt Up_Genes_EdgeR_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt LncRNA_GeneBody_Counting DiffExp_2e [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2e" [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: F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 304 Sep 16 10:45 /scratch/9373928.1.linga/Input/DiffExp_2e_Venn_Tables_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt -rw-r--r-- 1 kkarri waxmanlab 5088563 Sep 16 10:45 /scratch/9373928.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Sep 16 10:44 /scratch/9373928.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 5862 Sep 16 10:45 /scratch/9373928.1.linga/Input/Down_Genes_DESeq_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt -rw-r--r-- 1 kkarri waxmanlab 7903 Sep 16 10:45 /scratch/9373928.1.linga/Input/Down_Genes_EdgeR_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt -rw-r--r-- 1 kkarri waxmanlab 723008 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD2270.out -rw-r--r-- 1 kkarri waxmanlab 298 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD2270.summary -rw-r--r-- 1 kkarri waxmanlab 722678 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD2271.out -rw-r--r-- 1 kkarri waxmanlab 298 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD2271.summary -rw-r--r-- 1 kkarri waxmanlab 723496 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD2272.out -rw-r--r-- 1 kkarri waxmanlab 298 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD2272.summary -rw-r--r-- 1 kkarri waxmanlab 2805962 Sep 16 10:45 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD227_G170_M13M14M15_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2557034 Sep 16 10:45 /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD227_G170_M13M14M15_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 721518 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_Placebo_TD2270.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_Placebo_TD2270.summary -rw-r--r-- 1 kkarri waxmanlab 726746 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_Placebo_TD2271.out -rw-r--r-- 1 kkarri waxmanlab 298 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_Placebo_TD2271.summary -rw-r--r-- 1 kkarri waxmanlab 725261 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_Placebo_TD2272.out -rw-r--r-- 1 kkarri waxmanlab 298 Sep 16 10:44 /scratch/9373928.1.linga/Input/F_Placebo_TD2272.summary -rw-r--r-- 1 kkarri waxmanlab 2525 Sep 16 10:45 /scratch/9373928.1.linga/Input/Up_Genes_DESeq_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt -rw-r--r-- 1 kkarri waxmanlab 3470 Sep 16 10:45 /scratch/9373928.1.linga/Input/Up_Genes_EdgeR_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Sep 16 10:44 /scratch/9373928.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 42508 Sep 16 10:45 /scratch/9373928.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40588 Sep 16 10:45 /scratch/9373928.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 4968 Sep 16 10:44 /scratch/9373928.1.linga/Input/formatForSegex_ver3.R -rw-r--r-- 1 kkarri waxmanlab 815529 Sep 16 10:44 /scratch/9373928.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/9373928.1.linga/Input/F_CPA_4cycle_TD227: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:44 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:45 .. /scratch/9373928.1.linga/Input/F_Placebo_TD227: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:44 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:45 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Sep 16 10:45 . drwxrwxrwt. 14 root root 4.0K Sep 16 10:44 .. -rw-r--r-- 1 kkarri waxmanlab 132 Sep 16 10:44 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 147 Sep 16 10:44 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Sep 16 10:45 Input -rwxr-xr-x 1 kkarri waxmanlab 13K Sep 16 10:44 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Sep 16 10:44 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 22M drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 10:39 . drwxr-xr-x 8 kkarri waxmanlab 4.0K Sep 16 10:38 .. -rw-r--r-- 1 kkarri waxmanlab 304 Sep 16 10:39 DiffExp_2e_Venn_Tables_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.9M Sep 16 10:39 DiffExp_v2_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.8K Sep 16 10:39 Down_Genes_DESeq_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 7.8K Sep 16 10:39 Down_Genes_EdgeR_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.7M Sep 16 10:39 F_CPA_4cycle_TD227_G170_M13M14M15_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.5M Sep 16 10:39 F_CPA_4cycle_TD227_G170_M13M14M15_vs_F_Placebo_TD227_G170_M7M8M9_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.5K Sep 16 10:39 Up_Genes_DESeq_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.4K Sep 16 10:39 Up_Genes_EdgeR_LncRNA_GeneBody_F_CPA_4cycle_TD227_G170_M13M14M15_F_Placebo_TD227_G170_M7M8M9_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 42K Sep 16 10:39 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 40K Sep 16 10:39 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Sep 16 10:45:09 EDT 2019 0 minutes and 41 seconds elapsed. ==========================================================