----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G123_New_Env_PCA/Scripts/09b_DiffExp_1_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G123_New_Env_PCA Dataset_Label: G123 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: Male_3h_Vehicle_G123_M1M2 CONDITION_2_NAME: Male_3h_TCPOBOP_G123_M3M4 Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: Intron_Only_Regions_Lengths.txt COUNT_DIR: RefSeq_Intron_GTF OUTPUT_PREFIX: DiffExp_v2_Intronic_Only DiffExp_Index: DiffExp_1c COL_SUFFIX: Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Apr 15 18:51:13 EDT 2019 Running on node : scc-wh4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G123_New_Env_PCA/Scripts/09b_DiffExp_1_featureCounts Current job ID : 5223772 Current job name : Step_09b_DiffExp_1c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5223772.1.w Loading required modules... ------------------------------------------ Sample_DIR: G123_M1 Sample_ID: G123_M1 Description: Male_3h_Vehicle_1 M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G123_M1 Sample_DIR: G123_M2 Sample_ID: G123_M2 Description: Male_3h_Vehicle_2 M_Num: M2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G123_M2 M_Num_Cond1_List: M1M2 ------------------------------------------ ------------------------------------------ Sample_DIR: G123_M3 Sample_ID: G123_M3 Description: Male_3h_TCPOBOP_1 M_Num: M3 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G123_M3 Sample_DIR: G123_M4 Sample_ID: G123_M4 Description: Male_3h_TCPOBOP_2 M_Num: M4 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G123_M4 M_Num_Cond2_List: M3M4 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 2 NUM_REP_CONDITION1: 2 ========================================================== Renaming input count files Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. number of mapped reads 30619799 46696186 32796488 29093494 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 300238 Apr 15 18:51 /scratch/5223772.1.w/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 245870 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M40.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M40_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248438 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M41.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M41_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246405 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_Vehicle_G123_M1M20.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_Vehicle_G123_M1M20_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245535 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_Vehicle_G123_M1M21.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_Vehicle_G123_M1M21_num_mapped_reads.txt /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M4: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 18:51 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 18:51 .. /scratch/5223772.1.w/Input/Male_3h_Vehicle_G123_M1M2: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 18:51 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 18:51 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Male_3h_Vehicle_G123_M1M2 Male_3h_TCPOBOP_G123_M3M4 2 2 RefSeq_GeneBody.gtf /scratch/5223772.1.w/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt WARNING: ignoring environment value of R_HOME [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Male_3h_Vehicle_G123_M1M2" [1] "Male_3h_TCPOBOP_G123_M3M4" [1] 2 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/5223772.1.w/Input" [1] "DiffExp_v2_Intronic_Only" [1] "Intron_Only_Regions_Lengths.txt" [1] "sum1:NaN" "sum1:NaN" "sum1:NaN" [1] "sum2:NaN" "sum2:NaN" "sum2:NaN" load GTF file ... parse attributes ... [1] "output file is in: /scratch/5223772.1.w/Input/DiffExp_v2_Intronic_Only_Male_3h_Vehicle_G123_M1M2_Male_3h_TCPOBOP_G123_M3M4.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_Male_3h_Vehicle_G123_M1M2_Male_3h_TCPOBOP_G123_M3M4.txt Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only WARNING: ignoring environment value of R_HOME Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_Intronic_Only_Male_3h_Vehicle_G123_M1M2_Male_3h_TCPOBOP_G123_M3M4.txt Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only WARNING: ignoring environment value of R_HOME ========================================================== Comparison_Info: Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_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] "Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 71 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 20 7 [1] "Check out Up_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt!" [1] "Check out Down_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt!" Rscript Diff_Genes.R Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_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] "Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 89 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 36 7 [1] "Check out Up_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt!" [1] "Check out Down_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt Down_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt Intronic_Only_Counting DiffExp_1c WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1c" [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_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt Up_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt Intronic_Only_Counting DiffExp_1c WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1c" [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: Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 320 Apr 15 18:53 /scratch/5223772.1.w/Input/DiffExp_1c_Venn_Tables_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 7646648 Apr 15 18:52 /scratch/5223772.1.w/Input/DiffExp_v2_Intronic_Only_Male_3h_Vehicle_G123_M1M2_Male_3h_TCPOBOP_G123_M3M4.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Apr 15 18:51 /scratch/5223772.1.w/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 1950 Apr 15 18:52 /scratch/5223772.1.w/Input/Down_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 3673 Apr 15 18:52 /scratch/5223772.1.w/Input/Down_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Apr 15 18:51 /scratch/5223772.1.w/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 245870 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M40.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M40_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248438 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M41.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M41_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2378426 Apr 15 18:52 /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2378426 Apr 15 18:52 /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1652514 Apr 15 18:52 /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1652514 Apr 15 18:52 /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 246405 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_Vehicle_G123_M1M20.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_Vehicle_G123_M1M20_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245535 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_Vehicle_G123_M1M21.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:51 /scratch/5223772.1.w/Input/Male_3h_Vehicle_G123_M1M21_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 5212 Apr 15 18:52 /scratch/5223772.1.w/Input/Up_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 6653 Apr 15 18:52 /scratch/5223772.1.w/Input/Up_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Apr 15 18:51 /scratch/5223772.1.w/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 42223 Apr 15 18:53 /scratch/5223772.1.w/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 41009 Apr 15 18:53 /scratch/5223772.1.w/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Apr 15 18:51 /scratch/5223772.1.w/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Apr 15 18:51 /scratch/5223772.1.w/Input/formatForSegex_ver4.R /scratch/5223772.1.w/Input/Male_3h_TCPOBOP_G123_M3M4: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 18:51 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 18:53 .. /scratch/5223772.1.w/Input/Male_3h_Vehicle_G123_M1M2: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 18:51 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 18:53 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Apr 15 18:53 . drwxrwxrwt. 24 root root 20K Apr 15 18:51 .. -rw-r--r-- 1 kkarri waxmanlab 101 Apr 15 18:51 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 101 Apr 15 18:51 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Apr 15 18:53 Input -rw-r--r-- 1 kkarri waxmanlab 72M Apr 15 18:51 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Apr 15 18:51 differentialAnalysis.R ========================================================== Re-naming files in OUTPUT_DIR Need to append the COUNT_PROGRAM name to all output files List files in OUTPUT_DIR total 30M drwxr-sr-x 2 kkarri waxmanlab 4.0K Apr 15 18:48 . drwxr-sr-x 6 kkarri waxmanlab 4.0K Apr 15 18:46 .. -rw-r--r-- 1 kkarri waxmanlab 320 Apr 15 18:48 DiffExp_1c_Venn_Tables_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 7.3M Apr 15 18:48 DiffExp_v2_Intronic_Only_Male_3h_Vehicle_G123_M1M2_Male_3h_TCPOBOP_G123_M3M4_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.0K Apr 15 18:48 Down_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.6K Apr 15 18:48 Down_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 15 18:48 Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 15 18:48 Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M Apr 15 18:48 Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M Apr 15 18:48 Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.1K Apr 15 18:48 Up_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 6.5K Apr 15 18:48 Up_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_G123_M3M4_Male_3h_Vehicle_G123_M1M2_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 42K Apr 15 18:48 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 41K Apr 15 18:48 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Apr 15 18:53:24 EDT 2019 2 minutes and 11 seconds elapsed. ==========================================================