----------------------- 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_8_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_D1 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_8c COL_SUFFIX: Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Apr 22 14:43:50 EDT 2019 Running on node : scc-tm1 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09b_DiffExp_8_featureCounts Current job ID : 5505345 Current job name : Step_09b_DiffExp_8c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5505345.1.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_M10 Sample_ID: G168_G169_M10 Description: Met_EGFKO2_TCPO_D1 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M10 Sample_DIR: G168_G169_M11 Sample_ID: G168_G169_M11 Description: Met_EGFKO3_TCPO_D1 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M11 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 43096139 38750304 39184895 37682589 44304482 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 300238 Apr 22 14:43 /scratch/5505345.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 239568 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv0.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238643 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv1.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237788 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv2.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238720 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D10.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D10_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 239978 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D11.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D11_num_mapped_reads.txt /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 14:43 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 14:43 .. /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D1: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 14:43 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 14:43 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R MetEGFKO_F_Liv MetEGFKO_TCPO_D1 3 2 RefSeq_GeneBody.gtf /scratch/5505345.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "MetEGFKO_F_Liv" [1] "MetEGFKO_TCPO_D1" [1] 3 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/5505345.1.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/5505345.1.linga/Input/DiffExp_v2_Intronic_Only_MetEGFKO_F_Liv_MetEGFKO_TCPO_D1.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_MetEGFKO_F_Liv_MetEGFKO_TCPO_D1.txt MetEGFKO_TCPO_D1_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_D1.txt MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R MetEGFKO_TCPO_D1_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_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "MetEGFKO_TCPO_D1_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_D1_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] 200 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 137 7 [1] "Check out Up_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt!" Rscript Diff_Genes.R MetEGFKO_TCPO_D1_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_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "MetEGFKO_TCPO_D1_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_D1_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] 350 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 212 7 [1] "Check out Up_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D1_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_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt Down_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt Intronic_Only_Counting DiffExp_8c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_8c" [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_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt Up_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt Intronic_Only_Counting DiffExp_8c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_8c" [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_D1_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 325 Apr 22 14:45 /scratch/5505345.1.linga/Input/DiffExp_8c_Venn_Tables_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 7793295 Apr 22 14:45 /scratch/5505345.1.linga/Input/DiffExp_v2_Intronic_Only_MetEGFKO_F_Liv_MetEGFKO_TCPO_D1.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Apr 22 14:43 /scratch/5505345.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 18461 Apr 22 14:45 /scratch/5505345.1.linga/Input/Down_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 23607 Apr 22 14:45 /scratch/5505345.1.linga/Input/Down_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Apr 22 14:43 /scratch/5505345.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 239568 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv0.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238643 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv1.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237788 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv2.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238720 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D10.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D10_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 239978 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D11.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D11_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2378406 Apr 22 14:45 /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D1_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 2378406 Apr 22 14:45 /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D1_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 Apr 22 14:45 /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D1_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 1628297 Apr 22 14:45 /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D1_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 14401 Apr 22 14:45 /scratch/5505345.1.linga/Input/Up_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 25711 Apr 22 14:45 /scratch/5505345.1.linga/Input/Up_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Apr 22 14:43 /scratch/5505345.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 39972 Apr 22 14:45 /scratch/5505345.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 39221 Apr 22 14:45 /scratch/5505345.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Apr 22 14:43 /scratch/5505345.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Apr 22 14:43 /scratch/5505345.1.linga/Input/formatForSegex_ver4.R /scratch/5505345.1.linga/Input/MetEGFKO_F_Liv: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 14:43 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 14:45 .. /scratch/5505345.1.linga/Input/MetEGFKO_TCPO_D1: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 14:43 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 14:45 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Apr 22 14:45 . drwxrwxrwt. 21 root root 20K Apr 22 14:45 .. -rw-r--r-- 1 kkarri waxmanlab 162 Apr 22 14:43 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 127 Apr 22 14:43 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Apr 22 14:45 Input -rw-r--r-- 1 kkarri waxmanlab 72M Apr 22 14:43 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Apr 22 14:43 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 Apr 22 14:39 . drwxr-sr-x 6 kkarri waxmanlab 4.0K Apr 22 14:38 .. -rw-r--r-- 1 kkarri waxmanlab 325 Apr 22 14:39 DiffExp_8c_Venn_Tables_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 7.5M Apr 22 14:39 DiffExp_v2_Intronic_Only_MetEGFKO_F_Liv_MetEGFKO_TCPO_D1_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 19K Apr 22 14:39 Down_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 24K Apr 22 14:39 Down_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 22 14:39 MetEGFKO_TCPO_D1_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 2.3M Apr 22 14:39 MetEGFKO_TCPO_D1_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 Apr 22 14:39 MetEGFKO_TCPO_D1_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 Apr 22 14:39 MetEGFKO_TCPO_D1_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 15K Apr 22 14:39 Up_Genes_DESeq_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 26K Apr 22 14:39 Up_Genes_EdgeR_Intronic_Only_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 40K Apr 22 14:39 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 39K Apr 22 14:39 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Apr 22 14:45:26 EDT 2019 1 minutes and 36 seconds elapsed. ==========================================================