Question: SpliceR visualization tool
1
gravatar for Prasad
2.3 years ago by
Prasad1.6k
India
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 • 940 views
ADD COMMENTlink modified 20 months ago by kristoffer.vittingseerup1.8k • written 2.3 years ago by Prasad1.6k
1
gravatar for Carlo Yague
2.3 years ago by
Carlo Yague4.5k
Belgium
Carlo Yague4.5k 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 2.3 years ago • written 2.3 years ago by Carlo Yague4.5k

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 2.3 years ago by Prasad1.6k

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

ADD REPLYlink written 2.2 years ago by pilarcormo0

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

ADD REPLYlink written 2.2 years ago by Prasad1.6k
0
gravatar for kristoffer.vittingseerup
20 months ago by
European Union
kristoffer.vittingseerup1.8k wrote:

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

ADD COMMENTlink written 20 months ago by kristoffer.vittingseerup1.8k
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