Visualisation Of Alternative Splicing Events Using Rna-Seq Data

Question

[User 7998]

Hi,

I am looking for tools that provide a nice graphical display of different alternative splicing events for aligned and/or unaligned reads. I am already aware of Sircah but am looking for others please. Any suggestions would be appreciated.

regards

Kevin

[Fred]

How can you visualize alternative splicing events with unaligned reads? With aligned reads (in BAM format for example), I find IGV really good for that.

[Malachi Griffith]

A list of alternative splicing tools and resources can be found in this post: Recommended tools for alternative splicing detection from RNA-seq data

Answer 1

[brentp]

IGV can show splice junctions.

Even without the junctions.bed, you can set the reads track to show the "splice" between pairs (Right-click on your reads-track and set "Show as Pairs"). Between that and the coverage track, you can often see novel exons/splice junctions.

Answer 2

[Malachi Griffith]

In IGV 2.3.10 the Sashimi plot was introduced to help visualize splicing. Instructions on viewing can be found here: How can i visualize sashimi plots in IGV Genome Browser ?

Example:

Answer 3

[2184687-1231-83-]

Ensembl has a track from the Illumina Human Bodymap 2.0 that shows "intron RNAseq support". If it is configured to "Variable height" it gives a visual indication of how much RNAseq evidence has been mapped for each event. See for example the image below:

Answer 4

[Malachi Griffith]

In addition to IGV, another good next-gen genome browser capable of visualizing alternative splicing events in RNA-seq data is: Savant

Spliced reads are shown as grey bars below:

It has a plugin specifically created to enhance visualization of Cufflinks results.

Answer 5

[Gww]

GBrowse2 is quite nice for showing spliced RNA-seq reads. You can add a lot of additional custom tracks quite easily too.

Answer 6

[cmdcolin]

The sashimiplot plugin for jbrowse can be used to visualize junctions calculated directly from an RNA-seq BAM file or from a junctions.bed file outputted from tophat or similar https://github.com/elsiklab/sashimiplot

Answer 7

[Mark Rogers]

You may wish to give SpliceGrapher a try. It can display splice graphs similar to Sircah's along with depictions of splice junctions and RNA-Seq read coverage. We tried to make it easy to display multiple splice graphs on the same plot so you can make comparisons, e.g., between homologous genes or to compare AS for a gene for different variants/mutants.

You can find the sofware at splicegrapher.sf.net