Visualization of AS events files generated by rMATS in genome browser

[chisom Ezekannagha]

Hello,

Please I will like to know how i can be able to visualize the results of AS events generated by rMATS in a genome browser like jbrowse. Is there a possibility to convert the text files to a particular format accepted by the browser?

Else, can any member of the group suggest tools that will help me visualize the AS events file for easy interpretation of results or easy visualization of suggested AS events in the genome?  I am familiar with sashimi plot but I do the plot for all the genes i am working with. I will appreciate any help.

Thanks

Chisom

[Thomas Danhorn]

Hi Chisom,

I am not familiar with JBrowse, but if you search the internet for
"sashimi plot", you will find how to do it in the IGV browser or with a
stand-alone tool. You cannot feed the events directly to a browser or
tool, but you have to use the section of the BAM file where the event
happens (the chromosome and coordinates are in the results tables) to view
the alignment of the reads and create a sashimi plot.

Hope this helps,

Thomas

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[chisom Ezekannagha]

Hello Thomas,

Thanks and sorry for my late reply. 

I hope so too.

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[Shihao Shen]

Hi Chisom,

rMATS2sashimiplot provides an easy interface to illustrate the AS events in sashimi plots, although the results are in PDF and cannot be input into browser.

If you want to do it for all the events or all the genes, it will be much faster than generating the plots from IGV.

https://github.com/Xinglab/rmats2sashimiplot

Hope this helps,

Shihao Shen

rMATS Developer

Scientist II, Children's Hospital of Philadelphia

https://scholar.google.com/citations?user=VX7cW9cAAAAJ&hl=en

[chisom Ezekannagha]

Hello Shihao,

Yes, I know rMATS2sashimiplot provides an easy interface to illustrate the AS events but I have like over 70 genes for each events, will it be nice to do it for all the genes? 

Also the result generated in PDF, is it for a single gene or the plot represents a particular AS events? 

I really wanted to be able to visualize the events in a browser because I wanted to see it alongside an expression data.

regards,

Chisom 

[Shihao Shen]

Hi Chisom,

rMATS2sashimiplot can generate plots for all events, for both regions of the AS events only and the whole genes. For the whole gene plot, you need to extract the gene coordinates first and use the -c coordinate:annotaionFile mode.

Please feel free to let me know if you have any other questions.

Thanks,

Shihao

On Friday, March 22, 2019 at 11:40:44 AM UTC-4, chisom Ezekannagha wrote:

[chisom Ezekannagha]

Hello Shihao

I got this error while trying to run rMATS2sashimiplot for RI events.

Traceback (most recent call last):

  File "/usr/local/lib/python2.7/dist-packages/rmats2sashimiplot-2.0.2-py2.7.egg/MISO/misopy/sashimi_plot/sashimi_plot.py", line 11, in <module>

    import matplotlib

ImportError: No module named matplotlib

mv: cannot stat '/mnt/chisom/Testing/rMATS_sashimiplot/rmats2sashimiplot/RI_events_output/Sashimi_plot/chrChromosome08:30250007:30250354:+@chrChromosome08:30250007:30250714:+@chrChromosome08:30250427:30250714:+.pdf': No such file or directory

while I checked the sashimi_plot.py file and matplotlib was imported. Please do you know what might be causing the error? 

Thanks 

Chisom