RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Ballgown DE Visualization


RNA-seq_Flowchart4


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)).

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:

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)).