Question: Visualisation Of Alternative Splicing Events Using Rna-Seq Data
10
gravatar for User 7998
6.0 years ago by
User 7998130
User 7998130 wrote:

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

visualization rna rna-seq • 8.2k views
ADD COMMENTlink modified 9 months ago by cmdcolin510 • written 6.0 years ago by User 7998130
1

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.

ADD REPLYlink written 6.0 years ago by Fred640

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

ADD REPLYlink written 3.1 years ago by Malachi Griffith15k
10
gravatar for brentp
6.0 years ago by
brentp22k
Salt Lake City, UT
brentp22k wrote:

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.

ADD COMMENTlink written 6.0 years ago by brentp22k
4
gravatar for Malachi Griffith
3.4 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith15k wrote:

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:

enter image description here

ADD COMMENTlink written 3.4 years ago by Malachi Griffith15k
2
gravatar for 2184687-1231-83-
6.0 years ago by
2184687-1231-83-4.8k wrote:

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: alt text

ADD COMMENTlink written 6.0 years ago by 2184687-1231-83-4.8k
2
gravatar for Gww
6.0 years ago by
Gww2.6k
Canada
Gww2.6k wrote:

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

ADD COMMENTlink written 6.0 years ago by Gww2.6k
2
gravatar for Malachi Griffith
5.3 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith15k wrote:

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:

alt text

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

alt text

ADD COMMENTlink written 5.3 years ago by Malachi Griffith15k
1
gravatar for Mark Rogers
6.0 years ago by
Mark Rogers10
Mark Rogers10 wrote:

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

ADD COMMENTlink written 6.0 years ago by Mark Rogers10
1
gravatar for cmdcolin
9 months ago by
cmdcolin510
United States
cmdcolin510 wrote:

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

enter image description here

ADD COMMENTlink written 9 months ago by cmdcolin510
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