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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., 184.108.40.206)).
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., 220.127.116.11)).
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