SpliceR visualization tool

Question

[Prasad]

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.

Answer 1

[Carlo Yague]

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

[Prasad]

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

[pilarcormo]

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

[Prasad]

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

Answer 2

[Kristoffer Vitting-Seerup]

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