New version of rmats2sashimiplot released!

[Yi Xing]

Dear rMATS Users,

A brand-new version of rmats2sashimiplot has been released at https://github.com/Xinglab/rmats2sashimiplot. The program has been substantially re-written and refactored. Independent installation of MISO is no longer needed. Please try it out and send us feedback.

Yours,

Yi Xing

[Yi Xing]

Dear all,

An updated version of rmats2sashimiplot was uploaded to https://github.com/Xinglab/rmats2sashimiplot. This update enhances the plotting functions, including making "average" plots for groups of samples, which is useful for visualizing large datasets with many groups and replicates. See the attached figure for an example.

Cheers,

Yi Xing

[sridhar iyengar]

Thanks for this will try and keep you posted!

[Sam Harvey]

Hello Dr. Xing,

Thank you for this wonderful resource. I am confused about the PSI values reported in the attached plot. The reported Inclusion Levels for the top 3 samples in red are greater than 0.5 while the bottom 3 samples in yellow are less than 0.5. However the plot of the exonic reads as well as the PSI calculated from the junction reads suggests that the top 3 samples should have Inclusion Levels less than 0.5 and vice versa for the bottom three. Is it possible that the reported PSIs are switched?

This brings me to a more general question about where the PSI value for the rmats2sashimiplot is located. It seems like when rmats2sashimiplot is run in events mode, it takes the PSI from the provided rMATS output. However, no PSI is reported in coordinate mode. Since the junction reads are reported on the plot, would it be easy to use these reads to calculate PSI? I can't seem to find the file that stores the exon junction reads used to print the value in the plot within the rmats2sashimiplot directory.

Thanks for your help! I have also posted this request on the github.

Sincerely,

Sam

On Wednesday, March 15, 2017 at 2:47:36 PM UTC-5, Yi Xing wrote:

[Zhijie Xie (Jay)]

Hi Sam,

Thanks, I'm glad you use our tool. It turns out that the attached plot (i.e. rmats2sashimiplot.png) was plotted with wrong options. If you look at our Github page https://github.com/Xinglab/rmats2sashimiplot, the PSI values are ordered as you expected. Is not a bug, but a mistake in plotting this figure. Don't worry about it.

For the new feature you suggested, dev team are working on it.

在 2017年4月27日星期四 UTC+8上午6:43:43，Sam Harvey写道：

[Sam Harvey]

Thank you for the clarification, Jay. Much appreciated. Looking forward to future releases.

Sam

[ZHONG Huan]

Hi Dr. Xing, 

I cannot find the testdata. It seems like the old link is invalid.

http://www.mimg.ucla.edu/faculty/xing/rmats2sashimiplot/testData.tar

Thanks,

Best,

Huan

在 2017年2月15日星期三 UTC+8上午1:21:18，Yi Xing写道：

[Varun Gupta]

Hello Dr. Xing,
Thank you for the wonderful tool. I am having a slight issue in understanding the junction counts. If I look from the output of rMATS for Retained Intron(RI), the SJC are different from the one plotted on the graph. Is it because the junction counts are length normalized or something?

For example, look at this line from rMATS(RI)

1498    "ENSG00000255717.6"    "SNHG1"    chr11    -    62854887    62855216    62854887    62854938    62855132    62855216    1498    85,105    424,394    242,248    408,508    298    149    1.32027089261e-09    1.28921669158e-07    0.091,0.118    0.229,0.196    -0.108

In group1, I have SJC as 424 and 394, while group2 has SJC 408 and 508. But in grouping plot(see attached), I can see 448 for group1 and 489 for group2.
How are we reaching to this number.

Thanks for your help.

Regards
Varun