Skip to content

Latest commit

 

History

History
80 lines (56 loc) · 4.95 KB

DA_mRNA.md

File metadata and controls

80 lines (56 loc) · 4.95 KB
Raw

List of processes

DA_mRNA__doing_differential_analysis

Description

Differential gene expression analysis is carried out with sleuth.

Outputs

  • Sleuth R object: 1_Preprocessing/2_Differential_Analysis/mRNA__all_genes__rsleuth/${comparison}__mRNA_DEG_rsleuth.rds
  • Promoter of all detected genes: 1_Preprocessing/2_Differential_Analysis/mRNA__all_genes__bed_promoters/${comparison}__all_genes_prom.rds

DA_mRNA__plotting_differential_analysis_results

Description

This process makes standardized (i.e. similar types of plots are produced for mRNA-Seq data) PCA and volcano plots, and some other plots produced directly by sleuth.

Parameters

  • params.sleuth_plots__fdr_threshold: Peaks with FDR less than or equal to this value are colored in red in the volcano plot. Default: 0.05.
  • params.sleuth_plots__top_n_labels: The top n peaks with lowest FDR will have their annotated gene displayed on the volcano plot. Default: 15.

Outputs

  • Volcano plots:
    • Figures_Individual/2_Differential_Analysis/mRNA__volcano/${comparison}__mRNA_volcano.pdf
    • Figures_Merged/2_Differential_Analysis/mRNA__volcano.pdf.

  • PCA plots (PC 1 and 2):
    • Figures_Individual/2_Differential_Analysis/mRNA__PCA_1_2/${comparison}__mRNA_PCA_1_2.pdf.
    • Figures_Merged/2_Differential_Analysis/mRNA__PCA_1_2.pdf.
      • top left panel: percentage of variance explained by the top 5 first principal components
      • top right panel: PCA plot for principal components 1 and 2
      • bottom panels: genes annotated to peaks that contribute the most to principal components 1 (left) and 2 (right). Color code: red or -1 indicates that the peak is a positive contributor. Blue or +1 indicates that the peak is a negative contributor.

  • PCA plots (PC 3 and 4):
    • Figures_Individual/2_Differential_Analysis/mRNA__PCA_3_4/${comparison}__mRNA_PCA_3_4.pdf.
    • Figures_Merged/2_Differential_Analysis/mRNA__PCA_3_4.pdf.
      • Same as above but for principal components 3 and 4.

  • Other plots;
    • Figures_Individual/2_Differential_Analysis/mRNA__other_plots/${comparison}__mRNA_other_plots.pdf
    • Figures_Individual/2_Differential_Analysis/mRNA__other_plots/${comparison}__mRNA_other_plots.pdf

      • MA plot: Make an 'MA plot' for a given test. MA plots display, for each transcript, the mean of abundances across samples on the x-axis and fold change on the y-axis.

      • Density plot: Plot the density of a grouping.

DA_mRNA__saving_detailed_results_tables

Description

The detailed ATAC-seq results table is created in R, which gene id, name, coordinates, significance, log2 fold change and other sleuth columns.

Outputs

  • Tables_Individual/2_Differential_Analysis/mRNA_detailed/${comparison}__res_detailed_mRNA.{csv,xlsx}
  • Tables_Merged/2_Differential_Analysis/mRNA_detailed.{csv,xlsx}.