Question: Visualize Gene Fusions
1
gravatar for Ron
2.8 years ago by
Ron950
United States
Ron950 wrote:

Hi all,

Are there any tools to visualize gene fusion for evidence? Instead of loading the bam files and looking in IGV,if there was any method of automatically generating fusion evidence using the fusion results?I started using Oncofuse,but it does not give visual results.

Let me know.

Thanks,

Ron

rna-seq next-gen fusion R • 2.0k views
ADD COMMENTlink modified 12 months ago by pbpanigrahi180 • written 2.8 years ago by Ron950
1

have you tried some here. I haven't tried all but seem to be useful - Which program, tool, or strategy do you use to visualize genomic rearrangements?

ADD REPLYlink written 2.8 years ago by Amitm1.6k

If you are asking for visualization of the evidence then the answer of Malachi Griffith in the thread mentioned by @Amitm is what you need.

ADD REPLYlink written 2.6 years ago by mikhail.shugay3.3k
0
gravatar for Ron
2.6 years ago by
Ron950
United States
Ron950 wrote:

One of the packages could be used: http://gtrack.readthedocs.io/en/latest/index.html

ADD COMMENTlink written 2.6 years ago by Ron950
0
gravatar for ssv.bio
2.6 years ago by
ssv.bio180
ssv.bio180 wrote:

circos?

ADD COMMENTlink written 2.6 years ago by ssv.bio180
0
gravatar for pbpanigrahi
12 months ago by
pbpanigrahi180
pbpanigrahi180 wrote:

Although not direct answer to your question, I think you can explore FusionView module of FusionHub, a web server that allow you to have three different ways of visualizing fusion genes (Circos plot, Domain view and network view).

  1. In circos view you can have a global view of different chromosomes that are involved in fusion.
  2. In domain view, you can have an idea about different ways by which head and tail gene fuse together by varying their exons/domain combinations.
  3. Network view will show you a gene fusion network.

Hope this helps. Please provide your feedback/bug which will help to improve the tool.

Thanks

Priyabrata

ADD COMMENTlink written 12 months ago by pbpanigrahi180
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