DE Visualization

Malachi Griffith edited this page May 30, 2018 · 62 revisions

RNA-seq Flowchart - Module 4

3-iii. Ballgown DE Visualization

Navigate to the correct directory and then launch R:

cd $RNA_HOME/de/ballgown/ref_only
R

A separate R tutorial file has been provided in the github repo for part 2 of the tutorial: Tutorial_Part2_ballgown.R. Run the R commands detailed in the R script. All results are directed to pdf file(s). The output pdf files can be viewed in your browser at the following urls. Note, you must replace YOUR_IP_ADDRESS with your own amazon instance IP (e.g., 101.0.1.101)).

  • http://YOUR_IP_ADDRESS/rnaseq/de/ballgown/ref_only/Tutorial_Part2_ballgown_output.pdf

SUPPLEMENTARY R ANALYSIS

Occasionally you may wish to reformat and work with stringtie output in R manually. Therefore we provide an optional/advanced tutorial on how to format your results for R and perform "old school" (non-ballgown analysis) on your data.

In this tutorial you will:

  • Learn basic R usage and commands (common plots, and data manipulation tasks)
  • Examine the expression estimates
  • Create an MDS plot to visualize the differences between/among replicates, library prep methods and UHR versus HBR
  • Examine the differential expression estimates
  • Visualize the expression estimates and highlight those genes that appear to be differentially expressed
  • Generate a list of the top differentially expressed genes
  • Ask how reproducible technical replicates are.

Expression and differential expression files will be read into R. The R analysis will make use of the transcript-level expression and differential expression files from stringtie/ballgown. Navigate to the correct directory and then launch R:

cd $RNA_HOME/de/ballgown/ref_only/
R

A separate R file has been provided in the github repo for part 3 of the tutorial: Tutorial_Supplementary_R.R. Run the R commands detailed in the R script above.

The output file can be viewed in your browser at the following url. Note, you must replace YOUR_IP_ADDRESS with your own amazon instance IP (e.g., 101.0.1.101)).

  • http://YOUR_IP_ADDRESS/rnaseq/de/ballgown/ref_only/Tutorial_Part3_Supplementary_R_output.pdf
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