----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09b_DiffExp_10_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP Dataset_Label: G168_TCPO_Env GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: MetEGFKO_F_Liv CONDITION_2_NAME: MetEGFKO_TCPO_D5 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_10c COL_SUFFIX: Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed May 8 19:56:48 EDT 2019 Running on node : scc-kb6 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09b_DiffExp_10_featureCounts Current job ID : 6033232 Current job name : Step_09b_DiffExp_10c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6033232.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G168_G169_M4 Sample_ID: G168_G169_M4 Description: Met-EGFKO1-F-Liv M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M4 Sample_DIR: G168_G169_M5 Sample_ID: G168_G169_M5 Description: Met-EGFKO2-F-Liv M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M5 Sample_DIR: G168_G169_M6 Sample_ID: G168_G169_M6 Description: Met-EGFKO3-F-Liv M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M6 M_Num_Cond1_List: G169G169G169 ------------------------------------------ ------------------------------------------ Sample_DIR: G168_G169_M21 Sample_ID: G168_G169_M21 Description: Met-EGFKO1-TCPO-D5 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M21 Sample_DIR: G168_G169_M22 Sample_ID: G168_G169_M22 Description: Met-EGFKO2-TCPO-D5 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M22 M_Num_Cond2_List: G169G169 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 3 NUM_REP_CONDITION1: 3 ========================================================== 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. number of mapped reads 43161323 38784376 39214060 33350445 36603043 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 300238 May 8 19:59 /scratch/6033232.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 239568 May 8 19:58 /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 8 19:58 /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238643 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237788 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237413 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D50.out -rw-r--r-- 1 kkarri waxmanlab 9 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D50_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238819 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D51.out -rw-r--r-- 1 kkarri waxmanlab 9 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D51_num_mapped_reads.txt /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 8 19:59 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 8 19:59 .. /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D5: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 8 19:59 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 8 19:59 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R MetEGFKO_F_Liv MetEGFKO_TCPO_D5 3 2 RefSeq_GeneBody.gtf /scratch/6033232.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "MetEGFKO_F_Liv" [1] "MetEGFKO_TCPO_D5" [1] 3 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/6033232.1.linga/Input" [1] "DiffExp_v2_Intronic_Only" [1] "Intron_Only_Regions_Lengths.txt" [1] "sum1:NaN" "sum1:NaN" "sum1:NaN" "sum1:NaN" [1] "sum2:NaN" "sum2:NaN" "sum2:NaN" load GTF file ... parse attributes ... [1] "output file is in: /scratch/6033232.1.linga/Input/DiffExp_v2_Intronic_Only_MetEGFKO_F_Liv_MetEGFKO_TCPO_D5.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_MetEGFKO_F_Liv_MetEGFKO_TCPO_D5.txt MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_Intronic_Only_MetEGFKO_F_Liv_MetEGFKO_TCPO_D5.txt MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_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_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 348 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 278 7 [1] "Check out Up_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt!" Rscript Diff_Genes.R MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_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_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 511 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 365 7 [1] "Check out Up_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt Down_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt Intronic_Only_Counting DiffExp_10c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_10c" [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_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt Up_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt Intronic_Only_Counting DiffExp_10c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_10c" [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: MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 327 May 8 21:05 /scratch/6033232.1.linga/Input/DiffExp_10c_Venn_Tables_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 7827152 May 8 20:49 /scratch/6033232.1.linga/Input/DiffExp_v2_Intronic_Only_MetEGFKO_F_Liv_MetEGFKO_TCPO_D5.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 May 8 19:58 /scratch/6033232.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 51399 May 8 20:53 /scratch/6033232.1.linga/Input/Down_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 49965 May 8 20:54 /scratch/6033232.1.linga/Input/Down_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 300238 May 8 19:59 /scratch/6033232.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 239568 May 8 19:58 /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 8 19:58 /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238643 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237788 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237413 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D50.out -rw-r--r-- 1 kkarri waxmanlab 9 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D50_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238819 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D51.out -rw-r--r-- 1 kkarri waxmanlab 9 May 8 19:59 /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D51_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2378406 May 8 20:51 /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2426800 May 8 20:51 /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1628297 May 8 20:52 /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1676691 May 8 20:52 /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 25208 May 8 20:53 /scratch/6033232.1.linga/Input/Up_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 36946 May 8 20:54 /scratch/6033232.1.linga/Input/Up_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 May 8 19:58 /scratch/6033232.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 41063 May 8 21:00 /scratch/6033232.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40006 May 8 21:04 /scratch/6033232.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 May 8 19:58 /scratch/6033232.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 May 8 19:58 /scratch/6033232.1.linga/Input/formatForSegex_ver4.R /scratch/6033232.1.linga/Input/MetEGFKO_F_Liv: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 8 19:59 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 8 21:05 .. /scratch/6033232.1.linga/Input/MetEGFKO_TCPO_D5: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 8 19:59 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 8 21:05 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K May 8 21:05 . drwxrwxrwt. 73 root root 84K May 8 21:03 .. -rw-r--r-- 1 kkarri waxmanlab 162 May 8 19:58 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 127 May 8 19:58 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K May 8 21:05 Input -rw-r--r-- 1 kkarri waxmanlab 72M May 8 19:58 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K May 8 19:58 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 29M drwxr-sr-x 2 kkarri waxmanlab 4.0K May 8 20:59 . drwxr-sr-x 7 kkarri waxmanlab 4.0K May 8 19:57 .. -rw-r--r-- 1 kkarri waxmanlab 327 May 8 20:59 DiffExp_10c_Venn_Tables_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 7.5M May 8 20:59 DiffExp_v2_Intronic_Only_MetEGFKO_F_Liv_MetEGFKO_TCPO_D5_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 51K May 8 20:59 Down_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 49K May 8 20:59 Down_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M May 8 20:59 MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.4M May 8 20:59 MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M May 8 20:59 MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M May 8 20:59 MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 25K May 8 20:59 Up_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 37K May 8 20:59 Up_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 41K May 8 20:59 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 40K May 8 20:59 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Wed May 8 21:05:16 EDT 2019 68 minutes and 28 seconds elapsed. ==========================================================