search

qqwang-berkeley / JUM

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
MIT License
27 stars 11 forks source link

JUM output Splicing events Visualization tools #38

Closed shashibioinfo143 closed 3 years ago

shashibioinfo143 commented 3 years ago

Hi all,

greetings.

I was working on mRNA Splicing event analysis. I was using the JUM tool for mRNA splicing which gives 6 categories of splice patterns

for Visualizing these splice events I was looking for tools, came across IGV, LeafViz.

LeafViz is a Shiny app that is more interactive needs more scripting the inputs. moreover, LeafViz is part of Leafcutter it didn't accept other format files. I have started using LeafViz for JUM output files and I have troubleshooting errors that I encountered.

if anyone please let us know if it's possible to use JUM output files in Leafviz for the Visualization of splicing events or else please mention tools that are most useful for Visualization of Splice events.

Hope to hear good suggestions.

Thank you

qqwang-berkeley commented 3 years ago

Hi,

You can use iGV to visualize the splicing events identified by JUM, just simply feed iGV with your 2nd pass mapping bam files.

If you would like JUM to provide an output file compatible with LeafViz, could you send me a sample input file for LeafViz? I will add a code in the package to re-format a version of JUM output.

Qingqing

On Mon, May 24, 2021 at 9:26 AM shashibioinfo143 @.***> wrote:

Hi all,

greetings.

I was working on mRNA Splicing event analysis. I was using the JUM tool for mRNA splicing which gives 6 categories of splice patterns

for Visualizing these splice events I was looking for tools, came across IGV, LeafViz.

LeafViz is a Shiny app that is more interactive needs more scripting the inputs. moreover, LeafViz is part of Leafcutter it didn't accept other format files. I have started using LeafViz for JUM output files and I have troubleshooting errors that I encountered.

if anyone please let us know if it's possible to use JUM output files in Leafviz for the Visualization of splicing events or else please mention tools that are most useful for Visualization of Splice events.

Hope to hear good suggestions.

Thank you

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/qqwang-berkeley/JUM/issues/38, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGJ6PWZ4OS4BEXSZMQ3XEXLTPJHWXANCNFSM45NHM7RQ .