----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/08a_DiffExp_1_HTSeq Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation Dataset_Label: LZ GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: WT CONDITION_2_NAME: KcO 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: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed May 9 20:13:06 EDT 2018 Running on node : scc-kb8 Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/08a_DiffExp_1_HTSeq Current job ID : 6139524 Current job name : Step_08a_DiffExp_1c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6139524.1.linga Loading required modules... ------------------------------------------ Sample_DIR: LZ_M1 Sample_ID: LZ_M1 Description: WT1 M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M1 Sample_DIR: LZ_M2 Sample_ID: LZ_M2 Description: WT2 M_Num: M2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M2 Sample_DIR: LZ_M3 Sample_ID: LZ_M3 Description: WT3 M_Num: M3 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M3 Sample_DIR: LZ_M4 Sample_ID: LZ_M4 Description: WT4 M_Num: M4 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M4 Sample_DIR: LZ_M5 Sample_ID: LZ_M5 Description: WT5 M_Num: M5 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M5 Sample_DIR: LZ_M6 Sample_ID: LZ_M6 Description: WT6 M_Num: M6 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M6 Sample_DIR: Sample_ID: Description: M_Num: Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: M_Num_Cond1_List: M1M2M3M4M5M6 ------------------------------------------ ------------------------------------------ Sample_DIR: LZ_M7 Sample_ID: LZ_M7 Description: KO1 M_Num: M7 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M7 Sample_DIR: LZ_M8 Sample_ID: LZ_M8 Description: KO2 M_Num: M8 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M8 Sample_DIR: LZ_M9 Sample_ID: LZ_M9 Description: KO3 M_Num: M9 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M9 Sample_DIR: LZ_M10 Sample_ID: LZ_M10 Description: KO4 M_Num: M10 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M10 Sample_DIR: LZ_M11 Sample_ID: LZ_M11 Description: KO5 M_Num: M11 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M11 Sample_DIR: LZ_M12 Sample_ID: LZ_M12 Description: KO6 M_Num: M12 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M12 Sample_DIR: Sample_ID: Description: M_Num: Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: M_Num_Cond2_List: M7M8M9M10M11M12 ------------------------------------------ ========================================================== 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) 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 13897761 11055363 10476201 13531203 11649008 13929200 14386490 15289125 12749829 12358630 11759363 11908169 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 300238 May 9 20:13 /scratch/6139524.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 236719 May 9 20:13 /scratch/6139524.1.linga/Input/KcO0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/KcO0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 234423 May 9 20:13 /scratch/6139524.1.linga/Input/KcO1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/KcO1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235328 May 9 20:13 /scratch/6139524.1.linga/Input/KcO2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/KcO2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 236103 May 9 20:13 /scratch/6139524.1.linga/Input/KcO3.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/KcO3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235204 May 9 20:13 /scratch/6139524.1.linga/Input/KcO4.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/KcO4_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 236480 May 9 20:13 /scratch/6139524.1.linga/Input/KcO5.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/KcO5_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235913 May 9 20:13 /scratch/6139524.1.linga/Input/WT0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/WT0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237172 May 9 20:13 /scratch/6139524.1.linga/Input/WT1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/WT1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235857 May 9 20:13 /scratch/6139524.1.linga/Input/WT2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/WT2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 234735 May 9 20:13 /scratch/6139524.1.linga/Input/WT3.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/WT3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235197 May 9 20:13 /scratch/6139524.1.linga/Input/WT4.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/WT4_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235576 May 9 20:13 /scratch/6139524.1.linga/Input/WT5.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/WT5_num_mapped_reads.txt /scratch/6139524.1.linga/Input/KcO: total 12 drwxr-xr-x 2 kkarri waxmanlab 4096 May 9 20:13 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 9 20:13 .. -rw-r--r-- 1 kkarri waxmanlab 1 May 9 20:13 _num_mapped_reads.txt /scratch/6139524.1.linga/Input/WT: total 12 drwxr-xr-x 2 kkarri waxmanlab 4096 May 9 20:13 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 9 20:13 .. -rw-r--r-- 1 kkarri waxmanlab 1 May 9 20:13 _num_mapped_reads.txt ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WT KcO 6 6 RefSeq_GeneBody.gtf /scratch/6139524.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WT" [1] "KcO" [1] 6 [1] 6 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/6139524.1.linga/Input" [1] "DiffExp_v2_Intronic_Only" [1] "Intron_Only_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/6139524.1.linga/Input/DiffExp_v2_Intronic_Only_WT_KcO.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_WT_KcO.txt KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_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_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 39 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 35 7 [1] "Check out Up_Genes_DESeq_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt!" [1] "Check out Down_Genes_DESeq_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt!" Rscript Diff_Genes.R KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_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_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 59 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 55 7 [1] "Check out Up_Genes_EdgeR_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt!" [1] "Check out Down_Genes_EdgeR_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt Down_Genes_EdgeR_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt Intronic_Only_Counting DiffExp_1c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.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_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt Up_Genes_EdgeR_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt Intronic_Only_Counting DiffExp_1c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.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 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 320 May 9 20:16 /scratch/6139524.1.linga/Input/DiffExp_1c_Venn_Tables_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 10629240 May 9 20:15 /scratch/6139524.1.linga/Input/DiffExp_v2_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 May 9 20:13 /scratch/6139524.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 3894 May 9 20:16 /scratch/6139524.1.linga/Input/Down_Genes_DESeq_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 6580 May 9 20:16 /scratch/6139524.1.linga/Input/Down_Genes_EdgeR_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 300238 May 9 20:13 /scratch/6139524.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 236719 May 9 20:13 /scratch/6139524.1.linga/Input/KcO0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/KcO0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 234423 May 9 20:13 /scratch/6139524.1.linga/Input/KcO1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/KcO1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235328 May 9 20:13 /scratch/6139524.1.linga/Input/KcO2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/KcO2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 236103 May 9 20:13 /scratch/6139524.1.linga/Input/KcO3.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/KcO3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235204 May 9 20:13 /scratch/6139524.1.linga/Input/KcO4.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/KcO4_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 236480 May 9 20:13 /scratch/6139524.1.linga/Input/KcO5.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/KcO5_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 3297867 May 9 20:16 /scratch/6139524.1.linga/Input/KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 3467246 May 9 20:16 /scratch/6139524.1.linga/Input/KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 3533 May 9 20:16 /scratch/6139524.1.linga/Input/Up_Genes_DESeq_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 5504 May 9 20:16 /scratch/6139524.1.linga/Input/Up_Genes_EdgeR_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 May 9 20:13 /scratch/6139524.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 41079 May 9 20:16 /scratch/6139524.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 39569 May 9 20:16 /scratch/6139524.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 235913 May 9 20:13 /scratch/6139524.1.linga/Input/WT0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/WT0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237172 May 9 20:13 /scratch/6139524.1.linga/Input/WT1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/WT1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235857 May 9 20:13 /scratch/6139524.1.linga/Input/WT2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/WT2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 234735 May 9 20:13 /scratch/6139524.1.linga/Input/WT3.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/WT3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235197 May 9 20:13 /scratch/6139524.1.linga/Input/WT4.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/WT4_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235576 May 9 20:13 /scratch/6139524.1.linga/Input/WT5.out -rw-r--r-- 1 kkarri waxmanlab 9 May 9 20:13 /scratch/6139524.1.linga/Input/WT5_num_mapped_reads.txt -rwxr-xr-x 1 kkarri waxmanlab 3925 May 9 20:13 /scratch/6139524.1.linga/Input/formatForSegex_ver3.R /scratch/6139524.1.linga/Input/KcO: total 12 drwxr-xr-x 2 kkarri waxmanlab 4096 May 9 20:13 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 9 20:16 .. -rw-r--r-- 1 kkarri waxmanlab 1 May 9 20:13 _num_mapped_reads.txt /scratch/6139524.1.linga/Input/WT: total 12 drwxr-xr-x 2 kkarri waxmanlab 4096 May 9 20:13 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 9 20:16 .. -rw-r--r-- 1 kkarri waxmanlab 1 May 9 20:13 _num_mapped_reads.txt ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K May 9 20:16 . drwxrwxrwt. 71 root root 112K May 9 20:14 .. -rw-r--r-- 1 kkarri waxmanlab 132 May 9 20:13 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 138 May 9 20:13 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K May 9 20:16 Input -rw-r--r-- 1 kkarri waxmanlab 72M May 9 20:13 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 16K May 9 20:13 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 17M drwxr-sr-x 2 kkarri waxmanlab 32K May 9 20:16 . drwxr-sr-x 6 kkarri waxmanlab 32K May 9 20:13 .. -rw-r--r-- 1 kkarri waxmanlab 320 May 9 20:16 DiffExp_1c_Venn_Tables_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 11M May 9 20:16 DiffExp_v2_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 3.9K May 9 20:16 Down_Genes_DESeq_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 6.5K May 9 20:16 Down_Genes_EdgeR_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 3.2M May 9 20:16 KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 3.4M May 9 20:16 KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 3.5K May 9 20:16 Up_Genes_DESeq_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 5.4K May 9 20:16 Up_Genes_EdgeR_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 41K May 9 20:16 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 39K May 9 20:16 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Wed May 9 20:16:04 EDT 2018 2 minutes and 58 seconds elapsed. ==========================================================