----------------------- 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_6_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: WT_F_Liv CONDITION_2_NAME: WT_TCPO_D2 Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: Exon_Regions_Lengths.txt COUNT_DIR: RefSeq_Exon_GTF OUTPUT_PREFIX: DiffExp_v2_GeneBody DiffExp_Index: DiffExp_6a COL_SUFFIX: GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Apr 22 14:43:39 EDT 2019 Running on node : scc-tk3 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09b_DiffExp_6_featureCounts Current job ID : 5505328 Current job name : Step_09b_DiffExp_6a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5505328.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G168_G169_M1 Sample_ID: G168_G169_M1 Description: WT1_F_Liv M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M1 Sample_DIR: G168_G169_M2 Sample_ID: G168_G169_M2 Description: WT2_F_Liv M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M2 Sample_DIR: G168_G169_M3 Sample_ID: G168_G169_M3 Description: WT3_F_Liv M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M3 M_Num_Cond1_List: G169G169G169 ------------------------------------------ ------------------------------------------ Sample_DIR: G168_G169_M12 Sample_ID: G168_G169_M12 Description: WT1-TCPO-Day2 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M12 Sample_DIR: G168_G169_M13 Sample_ID: G168_G169_M13 Description: WT2-TCPO-Day2 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M13 Sample_DIR: G168_G169_M14 Sample_ID: G168_G169_M14 Description: WT3-TCPO-Day2 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M14 M_Num_Cond2_List: G169G169G169 ------------------------------------------ ========================================================== 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. Counting program: Not HTSeq No lines removed. number of mapped reads 30591403 41142742 38949776 35902972 39612567 40938936 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291522 Apr 22 14:43 /scratch/5505328.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 248319 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_F_Liv0.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_F_Liv0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 250134 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_F_Liv1.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_F_Liv1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249529 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_F_Liv2.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_F_Liv2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248970 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_TCPO_D20.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_TCPO_D20_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249852 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_TCPO_D21.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_TCPO_D21_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 250138 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_TCPO_D22.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_TCPO_D22_num_mapped_reads.txt /scratch/5505328.1.linga/Input/WT_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/5505328.1.linga/Input/WT_TCPO_D2: 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 WT_F_Liv WT_TCPO_D2 3 3 RefSeq_GeneBody.gtf /scratch/5505328.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WT_F_Liv" [1] "WT_TCPO_D2" [1] 3 [1] 3 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/5505328.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" [1] "sum1:240715.841051512" "sum1:233770.267807865" "sum1:237627.367629371" [4] "sum1:237371.158829583" [1] "sum2:241209.789852798" "sum2:239202.17774156" "sum2:243350.412438441" [4] "sum2:241254.1266776" load GTF file ... parse attributes ... [1] "output file is in: /scratch/5505328.1.linga/Input/DiffExp_v2_GeneBody_WT_F_Liv_WT_TCPO_D2.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_WT_F_Liv_WT_TCPO_D2.txt WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_GeneBody_WT_F_Liv_WT_TCPO_D2.txt WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_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_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 520 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 181 7 [1] "Check out Up_Genes_DESeq_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt!" Rscript Diff_Genes.R WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_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_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 702 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 375 7 [1] "Check out Up_Genes_EdgeR_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt Down_Genes_EdgeR_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt GeneBody_Counting DiffExp_6a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_6a" [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_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt Up_Genes_EdgeR_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt GeneBody_Counting DiffExp_6a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_6a" [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 #---------------------------------------------------------------------------------- Comparison_Info: WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 296 Apr 22 14:45 /scratch/5505328.1.linga/Input/DiffExp_6a_Venn_Tables_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 11239315 Apr 22 14:45 /scratch/5505328.1.linga/Input/DiffExp_v2_GeneBody_WT_F_Liv_WT_TCPO_D2.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Apr 22 14:43 /scratch/5505328.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 12930 Apr 22 14:45 /scratch/5505328.1.linga/Input/Down_Genes_DESeq_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 64495 Apr 22 14:45 /scratch/5505328.1.linga/Input/Down_Genes_EdgeR_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 291522 Apr 22 14:43 /scratch/5505328.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 38028 Apr 22 14:45 /scratch/5505328.1.linga/Input/Up_Genes_DESeq_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 51314 Apr 22 14:45 /scratch/5505328.1.linga/Input/Up_Genes_EdgeR_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Apr 22 14:43 /scratch/5505328.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 39713 Apr 22 14:45 /scratch/5505328.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40435 Apr 22 14:45 /scratch/5505328.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 248319 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_F_Liv0.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_F_Liv0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 250134 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_F_Liv1.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_F_Liv1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249529 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_F_Liv2.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_F_Liv2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248970 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_TCPO_D20.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_TCPO_D20_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249852 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_TCPO_D21.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_TCPO_D21_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 250138 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_TCPO_D22.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 22 14:43 /scratch/5505328.1.linga/Input/WT_TCPO_D22_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2426753 Apr 22 14:45 /scratch/5505328.1.linga/Input/WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2450950 Apr 22 14:45 /scratch/5505328.1.linga/Input/WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 2378357 Apr 22 14:45 /scratch/5505328.1.linga/Input/WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2402554 Apr 22 14:45 /scratch/5505328.1.linga/Input/WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR.txt -rwxr-xr-x 1 kkarri waxmanlab 3925 Apr 22 14:43 /scratch/5505328.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Apr 22 14:43 /scratch/5505328.1.linga/Input/formatForSegex_ver4.R /scratch/5505328.1.linga/Input/WT_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/5505328.1.linga/Input/WT_TCPO_D2: 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. 13 root root 20K Apr 22 14:44 .. -rw-r--r-- 1 kkarri waxmanlab 141 Apr 22 14:43 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 159 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 30M 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 296 Apr 22 14:39 DiffExp_6a_Venn_Tables_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 11M Apr 22 14:39 DiffExp_v2_GeneBody_WT_F_Liv_WT_TCPO_D2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 13K Apr 22 14:39 Down_Genes_DESeq_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 63K Apr 22 14:39 Down_Genes_EdgeR_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 38K Apr 22 14:39 Up_Genes_DESeq_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 51K Apr 22 14:39 Up_Genes_EdgeR_GeneBody_WT_TCPO_D2_G168_TCPO_Env_G169G169G169_WT_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 39K Apr 22 14:39 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 40K Apr 22 14:39 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 2.4M Apr 22 14:39 WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.4M Apr 22 14:39 WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 22 14:39 WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 22 14:39 WT_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_WT_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR_featureCounts.txt ========================================================== ========================================================== Finished on : Mon Apr 22 14:45:24 EDT 2019 1 minutes and 45 seconds elapsed. ==========================================================