Any tool to detect differential splicing of a gene between samples?

Question

[Apex92]

Hi all - is there any well know software or a website that can check for significant alternative events (different splicing junctions) of a gene?

I have RNA-seq data and I am focusing on comparing alternative events of specific genes in two different BAM files.

I have worked with MISO and it works fines with until comparing two BAM files using compare_miso. I get the error below when I want to filter events by bayes-factor using filter_events I do get this error

Note: This utility only works on MISO output for two-isoform event annotations. Error: filter_events.py is only defined for MISO output on two-isoform alternative events. Found a non-two isoform event: ENSMUSG00000048285.9

Apart from the error mentioned above, I do get this error when trying to draw a sashimi plot by MISO:

home/pachecop/pachecop/splicing/BamFiles/myenv/lib/python2.7/site-packages/matplotlib/cbook/deprecation.py:106: MatplotlibDeprecationWarning: The mpl_toolkits.axes_grid module was deprecated in version 2.1. Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist provies the same functionality instead.warnings.warn(message, mplDeprecation, stacklevel=1)

Unfortunately, I do not know how to solve the problems - can anyone help me with introducing an alternative tool or a suggestion to solve the problems? Any help is appreciated - thank you.

Answer 1

[Kristoffer Vitting-Seerup]

I wrote a summary of the major approaches and tools here - hope it helps.

Cheers Kristoffer

[Apex92]

A great source thank you - I decided to use rMATS.

Answer 2

[Peter]

it isnt quite what you asked, but this does detect differential exon usage between conditions, which if you are clever .... https://bioconductor.org/packages/devel/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html the documentation is good and, why not.