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Visualization of RNA-Seq results with CummeRbund

Contributors

Andrea Bagnacani

Questions

Objectives

last_modification Last modification: Oct 9, 2018

Why visualization?

Speaker Notes Data alone does not bring any information: to carry information, data needs to be contextualized. Transcriptomic data is no exception, therefore to organize the growing body of knowledge pertaining RNA-Seq experiments and infer valuable insights, data needs to be organized, annotated, and ultimately visualized.


Where is my data coming from?

Wang et al, Nat Rev Genet, 2009

Wang et al, Nat Rev Genet, 2009

Speaker Notes

This is the process that will:

But once this pipeline is implemented, how are sequence data going to be analysed and managed?


Bioinformatic tools for RNA-Seq analysis

Once the RNA-Seq pipeline is implemented, we still need to handle and analyse all data that is generated. This requires:


Bioinformatic tools for RNA-Seq analysis

Trapnell et al, Nat Protoc, 2012

Trapnell et al, Nat Protoc, 2012 Speaker Notes


Bioinformatic tools for RNA-Seq analysis

The last step in our RNA-Seq analysis is CuffDiff. Its output comprises multiple files containing the results of the differential expression analysis.

Speaker Notes


Bioinformatic tools for RNA-Seq analysis

Whatever storage strategy you opted for, i.e. multiple tab-separated-value files or a SQLite database, all data is still retained within text format.

We need to have a bird’s-eye view of that data, and make sense of it


Visualization


CummeRbund

CummeRbund is an R package for visualizing the results of a CuffDiff output.


CummeRbund

CummeRbund needs to be instructed on which data to be visualized:


CummeRbund

Once the most significant differentially expressed gene has been identified, CummeRbund can generate publication-ready plots to highlight…

.image-50[CummeRbund Expression plot]

The expression of all isoforms of the single gene with replicate FPKMs


CummeRbund

Once the most significant differentially expressed gene has been identified, CummeRbund can generate publication-ready plots to highlight…

.image-50[CummeRbund Expression plot]

The expression bar-plot of all isoforms of a gene with replicate FPKMs


CummeRbund

…and many more

.image-50[Other CummeRbund plots]

Have a look at CummerBund’s tutorial to overview all possibilities!


Key Points

Thank you!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors! Galaxy Training Network This material is licensed under the Creative Commons Attribution 4.0 International License.