----------------------- 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/08b_DiffExp_12_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana Dataset_Label: GSE118757 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: Ezh12 CONDITION_2_NAME: M2Ezh12 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_12c COL_SUFFIX: Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 10 14:05:46 EDT 2020 Running on node : scc-kb8 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08b_DiffExp_12_featureCounts Current job ID : 3784407 Current job name : Step_08b_DiffExp_12c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3784407.1.linga Loading required modules... ------------------------------------------ Sample_DIR: Ezh12M_1 Sample_ID: Ezh12M_1 Description: Ezh12M_1 M_Num: 1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: Ezh12M_1 Sample_DIR: Ezh12M_2 Sample_ID: Ezh12M_2 Description: Ezh12M_2 M_Num: 2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: Ezh12M_2 Sample_DIR: Ezh12F_1 Sample_ID: Ezh12F_1 Description: Ezh12F_1 M_Num: 1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: Ezh12F_1 Sample_DIR: Ezh12F_2 Sample_ID: Ezh12F_2 Description: Ezh12F_2 M_Num: 2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: Ezh12F_2 Sample_DIR: Ezh12F_3 Sample_ID: Ezh12F_3 Description: Ezh12F_3 M_Num: 3 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: Ezh12F_3 Sample_DIR: Ezh12F_4 Sample_ID: Ezh12F_4 Description: Ezh12F_4 M_Num: 4 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: Ezh12F_4 Sample_DIR: Ezh12F_5 Sample_ID: Ezh12F_5 Description: Ezh12F_5 M_Num: 5 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: Ezh12F_5 M_Num_Cond1_List: 1212345 ------------------------------------------ ------------------------------------------ Sample_DIR: M2Ezh12M_1 Sample_ID: M2Ezh12M_1 Description: M2Ezh12M_1 M_Num: 1 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: M2Ezh12M_1 Sample_DIR: M2Ezh12M_2 Sample_ID: M2Ezh12M_2 Description: M2Ezh12M_2 M_Num: 2 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: M2Ezh12M_2 Sample_DIR: M2Ezh12M_3 Sample_ID: M2Ezh12M_3 Description: M2Ezh12M_3 M_Num: 3 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: M2Ezh12M_3 Sample_DIR: M2Ezh12F_1 Sample_ID: M2Ezh12F_1 Description: M2Ezh12F_1 M_Num: 1 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: M2Ezh12F_1 Sample_DIR: M2Ezh12F_2 Sample_ID: M2Ezh12F_2 Description: M2Ezh12F_2 M_Num: 2 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: M2Ezh12F_2 Sample_DIR: M2Ezh12F_3 Sample_ID: M2Ezh12F_3 Description: M2Ezh12F_3 M_Num: 3 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: M2Ezh12F_3 M_Num_Cond2_List: 123123 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 7 NUM_REP_CONDITION1: 7 ========================================================== 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. 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. 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. Counting program: Not HTSeq No lines removed. number of mapped reads 17458557 19999815 19216346 20730440 18248587 18376843 18963942 37648013 18553680 16317811 17521399 17379424 9182533 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 241718 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh120.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh120_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241150 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh121.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh121_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238866 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh122.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh122_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238566 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh123.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh123_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 239603 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh124.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh124_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238096 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh125.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh125_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237546 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh126.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh126_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Mar 10 14:05 /scratch/3784407.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 244123 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh120.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh120_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 240502 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh121.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh121_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 236823 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh122.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh122_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 242107 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh123.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh123_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 240403 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh124.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh124_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235314 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh125.out -rw-r--r-- 1 kkarri waxmanlab 8 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh125_num_mapped_reads.txt /scratch/3784407.1.linga/Input/Ezh12: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:05 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:05 .. /scratch/3784407.1.linga/Input/M2Ezh12: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:05 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:05 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Ezh12 M2Ezh12 7 6 RefSeq_GeneBody.gtf /scratch/3784407.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Ezh12" [1] "M2Ezh12" [1] 7 [1] 6 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/3784407.1.linga/Input" [1] "DiffExp_v2_Intronic_Only" [1] "Intron_Only_Regions_Lengths.txt" [1] "sum1:NaN" "sum1:NaN" "sum1:NaN" "sum1:NaN" "sum1:NaN" "sum1:NaN" "sum1:NaN" [8] "sum1:NaN" [1] "sum2:NaN" "sum2:NaN" "sum2:NaN" "sum2:NaN" "sum2:NaN" "sum2:NaN" "sum2:NaN" load GTF file ... parse attributes ... [1] "output file is in: /scratch/3784407.1.linga/Input/DiffExp_v2_Intronic_Only_Ezh12_M2Ezh12.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_Ezh12_M2Ezh12.txt M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_Intronic_Only_Ezh12_M2Ezh12.txt M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_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_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 622 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 666 7 [1] "Check out Up_Genes_DESeq_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt!" [1] "Check out Down_Genes_DESeq_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt!" Rscript Diff_Genes.R M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_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_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 619 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 681 7 [1] "Check out Up_Genes_EdgeR_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt!" [1] "Check out Down_Genes_EdgeR_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt Down_Genes_EdgeR_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt Intronic_Only_Counting DiffExp_12c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_12c" [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_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt Up_Genes_EdgeR_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt Intronic_Only_Counting DiffExp_12c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_12c" [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 328 Mar 10 14:07 /scratch/3784407.1.linga/Input/DiffExp_12c_Venn_Tables_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt -rw-r--r-- 1 kkarri waxmanlab 14152293 Mar 10 14:07 /scratch/3784407.1.linga/Input/DiffExp_v2_Intronic_Only_Ezh12_M2Ezh12.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Mar 10 14:05 /scratch/3784407.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 96617 Mar 10 14:07 /scratch/3784407.1.linga/Input/Down_Genes_DESeq_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt -rw-r--r-- 1 kkarri waxmanlab 91289 Mar 10 14:07 /scratch/3784407.1.linga/Input/Down_Genes_EdgeR_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt -rw-r--r-- 1 kkarri waxmanlab 241718 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh120.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh120_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241150 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh121.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh121_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238866 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh122.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh122_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238566 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh123.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh123_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 239603 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh124.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh124_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238096 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh125.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh125_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237546 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh126.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/Ezh126_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Mar 10 14:05 /scratch/3784407.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 244123 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh120.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh120_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 240502 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh121.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh121_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 236823 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh122.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh122_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 242107 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh123.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh123_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 240403 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh124.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh124_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235314 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh125.out -rw-r--r-- 1 kkarri waxmanlab 8 Mar 10 14:05 /scratch/3784407.1.linga/Input/M2Ezh125_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 4725497 Mar 10 14:07 /scratch/3784407.1.linga/Input/M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 5790165 Mar 10 14:07 /scratch/3784407.1.linga/Input/M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 4023782 Mar 10 14:07 /scratch/3784407.1.linga/Input/M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 5088450 Mar 10 14:07 /scratch/3784407.1.linga/Input/M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 105257 Mar 10 14:07 /scratch/3784407.1.linga/Input/Up_Genes_DESeq_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt -rw-r--r-- 1 kkarri waxmanlab 131387 Mar 10 14:07 /scratch/3784407.1.linga/Input/Up_Genes_EdgeR_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Mar 10 14:05 /scratch/3784407.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 43701 Mar 10 14:07 /scratch/3784407.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 42923 Mar 10 14:07 /scratch/3784407.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Mar 10 14:05 /scratch/3784407.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Mar 10 14:05 /scratch/3784407.1.linga/Input/formatForSegex_ver4.R /scratch/3784407.1.linga/Input/Ezh12: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:05 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:07 .. /scratch/3784407.1.linga/Input/M2Ezh12: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:05 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:07 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Mar 10 14:07 . drwxrwxrwt. 26 root root 4.0K Mar 10 14:07 .. -rw-r--r-- 1 kkarri waxmanlab 222 Mar 10 14:05 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 231 Mar 10 14:05 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 10 14:07 Input -rw-r--r-- 1 kkarri waxmanlab 72M Mar 10 14:05 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Mar 10 14:05 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 73M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 10 14:00 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 10 13:58 .. -rw-r--r-- 1 kkarri waxmanlab 328 Mar 10 14:00 DiffExp_12c_Venn_Tables_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 14M Mar 10 14:00 DiffExp_v2_Intronic_Only_Ezh12_M2Ezh12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 95K Mar 10 14:00 Down_Genes_DESeq_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 90K Mar 10 14:00 Down_Genes_EdgeR_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.6M Mar 10 14:00 M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.6M Mar 10 14:00 M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.9M Mar 10 14:00 M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.9M Mar 10 14:00 M2Ezh12_GSE118757_123123_vs_Ezh12_GSE118757_1212345_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 103K Mar 10 14:00 Up_Genes_DESeq_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 129K Mar 10 14:00 Up_Genes_EdgeR_Intronic_Only_M2Ezh12_GSE118757_123123_Ezh12_GSE118757_1212345_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 43K Mar 10 14:00 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 42K Mar 10 14:00 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Tue Mar 10 14:08:02 EDT 2020 2 minutes and 16 seconds elapsed. ==========================================================