Question: SpliceR visualization tool
gravatar for Prasad
3.7 years ago by
Prasad1.6k wrote:

Dear all,

i have performed alternate splicing analysis using SpliceR. I want to visualize these splicing event results. Are there any tool to visualize spliceR results.

There are many tools like SplicingViewer [download link is not working], SpliceSeq, Manananggal etc which requires re-analysis.

Any help to specifically visualize SpliceR data.

splice rna-seq tool R • 1.3k views
ADD COMMENTlink modified 3.1 years ago by kristoffer.vittingseerup3.4k • written 3.7 years ago by Prasad1.6k
gravatar for Carlo Yague
3.7 years ago by
Carlo Yague5.2k
Carlo Yague5.2k wrote:

Have you looked at the SpliceR vignette ? They show how to make Venn diagrams to analyse results.

After running spliceR(), annotating the spliceRlist object with information about alterna- tive splicing events. the spliceRPlot() function can be used for initial data exploration. spliceRPlot() generates a range of Venn diagrams, with one circle per condition, analyzing different aspects of the data.

They also explain how to generate a GTF file to visualize the transcript models in a genome browser :

After running assembly with cufflinks or another assembler, and perhaps spliceR() and/or annotatePTC(), visualization of trancripts in genome browsers is often helpful. To facilitate this, spliceR provides the generateGTF function

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Carlo Yague5.2k

thanks i will try generateGTF. In my case venn is of no use. I want to visualize all the splicing events across different transcripts of a gene

ADD REPLYlink written 3.7 years ago by Prasad1.6k

Hi, did you manage to visualise the GTF files obtained from SpliceR? Thanks!

ADD REPLYlink written 3.6 years ago by pilarcormo0

Tried but couldn't get the desire result means failed to visualize splicing events what was reported.

ADD REPLYlink written 3.6 years ago by Prasad1.6k
gravatar for kristoffer.vittingseerup
3.1 years ago by
European Union
kristoffer.vittingseerup3.4k wrote:

Sound like you rather want to do is a sashimi plot - see fx the IGV plugin then using spliceR

ADD COMMENTlink written 3.1 years ago by kristoffer.vittingseerup3.4k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2363 users visited in the last hour