----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/09a_DiffExp_1_HTSeq Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline Dataset_Label: IP_Saline GTF_Files_DIR: /restricted/projectnb/waxmanlab/kkarri/GTF_Files1 ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: Control CONDITION_2_NAME: THIOACETAMIDE Lengths_DIR: /restricted/projectnb/waxmanlab/kkarri/GTF_Files1/lengths GENE_LENGTHS_FILE: Exon_Regions_Lengths.txt COUNT_DIR: RefSeq_Exon_GTF OUTPUT_PREFIX: DiffExp_v2_GeneBody DiffExp_Index: DiffExp_1a COL_SUFFIX: GeneBody COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Thu Jun 22 16:58:05 EDT 2017 Running on node : scc-tm3 Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/09a_DiffExp_1_HTSeq Current job ID : 9501378 Current job name : Step_09a_DiffExp_1a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9501378.1.linga Loading required modules... ------------------------------------------ Sample_DIR: C_IP1 Sample_ID: C_IP1 Description: C_IP1 M_Num: IP1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_IP1 Sample_DIR: C_IP2 Sample_ID: C_IP2 Description: C_IP2 M_Num: IP2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_IP2 Sample_DIR: C_IP3 Sample_ID: C_IP3 Description: C_IP3 M_Num: IP3 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_IP3 Sample_DIR: C_IP4 Sample_ID: C_IP4 Description: C_IP4 M_Num: IP4 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_IP4 Sample_DIR: C_IP5 Sample_ID: C_IP5 Description: C_IP5 M_Num: IP5 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_IP5 Sample_DIR: C_IP6 Sample_ID: C_IP6 Description: C_IP6 M_Num: IP6 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_IP6 M_Num_Cond1_List: IP1IP2IP3IP4IP5IP6 ------------------------------------------ ------------------------------------------ Sample_DIR: TA_IP1 Sample_ID: TA_IP1 Description: TA_IP1 M_Num: IP1 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: TA_IP1 Sample_DIR: TA_IP2 Sample_ID: TA_IP2 Description: TA_IP2 M_Num: IP2 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: TA_IP2 Sample_DIR: TA_IP3 Sample_ID: TA_IP3 Description: TA_IP3 M_Num: IP3 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: TA_IP3 M_Num_Cond2_List: IP1IP2IP3 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 6 NUM_REP_CONDITION1: 6 ========================================================== Renaming input count files Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) number of mapped reads 33956871 33447956 29272003 26344375 79664742 30226350 30260149 30669049 30202146 ========================================================== List files in Input -rw-r--r-- 1 kkarri montilab-p 169507 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control0.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control0_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 169295 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control1.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control1_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 168314 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control2.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control2_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 167750 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control3.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control3_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 173225 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control4.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control4_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 167863 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control5.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control5_num_mapped_reads.txt -rwx------ 1 kkarri montilab-p 197610 Jun 22 16:58 /scratch/9501378.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri montilab-p 169700 Jun 22 16:58 /scratch/9501378.1.linga/Input/THIOACETAMIDE0.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/THIOACETAMIDE0_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 170059 Jun 22 16:58 /scratch/9501378.1.linga/Input/THIOACETAMIDE1.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/THIOACETAMIDE1_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 169992 Jun 22 16:58 /scratch/9501378.1.linga/Input/THIOACETAMIDE2.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/THIOACETAMIDE2_num_mapped_reads.txt /scratch/9501378.1.linga/Input/Control: total 8 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 22 16:58 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 22 16:58 .. /scratch/9501378.1.linga/Input/THIOACETAMIDE: total 8 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 22 16:58 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 22 16:58 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Control THIOACETAMIDE 6 3 RefSeq_GeneBody.gtf /scratch/9501378.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Control" [1] "THIOACETAMIDE" [1] 6 [1] 3 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/9501378.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/9501378.1.linga/Input/DiffExp_v2_GeneBody_Control_THIOACETAMIDE.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_Control_THIOACETAMIDE.txt THIOACETAMIDE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R THIOACETAMIDE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "THIOACETAMIDE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 843 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 763 7 [1] "Check out Up_Genes_DESeq_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt!" Rscript Diff_Genes.R THIOACETAMIDE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "THIOACETAMIDE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 996 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 816 7 [1] "Check out Up_Genes_EdgeR_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt Down_Genes_EdgeR_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt GeneBody_Counting DiffExp_1a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1a" [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_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt Up_Genes_EdgeR_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt GeneBody_Counting DiffExp_1a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1a" [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 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri montilab-p 169507 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control0.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control0_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 169295 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control1.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control1_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 168314 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control2.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control2_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 167750 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control3.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control3_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 173225 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control4.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control4_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 167863 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control5.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/Control5_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 295 Jun 22 16:59 /scratch/9501378.1.linga/Input/DiffExp_1a_Venn_Tables_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt -rw-r--r-- 1 kkarri montilab-p 7967767 Jun 22 16:59 /scratch/9501378.1.linga/Input/DiffExp_v2_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt -rwxr-xr-x 1 kkarri montilab-p 7394 Jun 22 16:58 /scratch/9501378.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri montilab-p 56898 Jun 22 16:59 /scratch/9501378.1.linga/Input/Down_Genes_DESeq_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt -rw-r--r-- 1 kkarri montilab-p 114700 Jun 22 16:59 /scratch/9501378.1.linga/Input/Down_Genes_EdgeR_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt -rwx------ 1 kkarri montilab-p 197610 Jun 22 16:58 /scratch/9501378.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri montilab-p 169700 Jun 22 16:58 /scratch/9501378.1.linga/Input/THIOACETAMIDE0.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/THIOACETAMIDE0_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 170059 Jun 22 16:58 /scratch/9501378.1.linga/Input/THIOACETAMIDE1.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/THIOACETAMIDE1_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 169992 Jun 22 16:58 /scratch/9501378.1.linga/Input/THIOACETAMIDE2.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 16:58 /scratch/9501378.1.linga/Input/THIOACETAMIDE2_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 1709903 Jun 22 16:59 /scratch/9501378.1.linga/Input/THIOACETAMIDE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri montilab-p 1744577 Jun 22 16:59 /scratch/9501378.1.linga/Input/THIOACETAMIDE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri montilab-p 59560 Jun 22 16:59 /scratch/9501378.1.linga/Input/Up_Genes_DESeq_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt -rw-r--r-- 1 kkarri montilab-p 72312 Jun 22 16:59 /scratch/9501378.1.linga/Input/Up_Genes_EdgeR_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt -rwxr-xr-x 1 kkarri montilab-p 9553 Jun 22 16:58 /scratch/9501378.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri montilab-p 39606 Jun 22 16:59 /scratch/9501378.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri montilab-p 40846 Jun 22 16:59 /scratch/9501378.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri montilab-p 3925 Jun 22 16:58 /scratch/9501378.1.linga/Input/formatForSegex_ver3.R /scratch/9501378.1.linga/Input/Control: total 8 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 22 16:58 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 22 16:59 .. /scratch/9501378.1.linga/Input/THIOACETAMIDE: total 8 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 22 16:58 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 22 16:59 .. ========================================================== List files in scratch total 41M drwxr-xr-x 3 kkarri montilab-p 4.0K Jun 22 16:59 . drwxrwxrwt. 12 root root 20K Jun 22 16:58 .. -rw-r--r-- 1 kkarri montilab-p 141 Jun 22 16:58 Condition_1.txt -rw-r--r-- 1 kkarri montilab-p 96 Jun 22 16:58 Condition_2.txt drwxr-xr-x 4 kkarri montilab-p 4.0K Jun 22 16:59 Input -rwx------ 1 kkarri montilab-p 41M Jun 22 16:58 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri montilab-p 16K Jun 22 16:58 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 6.1M drwxr-sr-x 2 kkarri waxmanlab 32K Jun 22 16:59 . drwxr-sr-x 6 kkarri waxmanlab 32K Jun 22 16:58 .. -rw-r--r-- 1 kkarri waxmanlab 295 Jun 22 16:59 DiffExp_1a_Venn_Tables_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 7.6M Jun 22 16:59 DiffExp_v2_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 56K Jun 22 16:59 Down_Genes_DESeq_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 113K Jun 22 16:59 Down_Genes_EdgeR_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 1.7M Jun 22 16:59 THIOACETAMIDE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 1.7M Jun 22 16:59 THIOACETAMIDE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 59K Jun 22 16:59 Up_Genes_DESeq_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 71K Jun 22 16:59 Up_Genes_EdgeR_GeneBody_THIOACETAMIDE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 39K Jun 22 16:59 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40K Jun 22 16:59 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Thu Jun 22 16:59:27 EDT 2017 1 minutes and 22 seconds elapsed. ==========================================================