Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq data

Question

[ntsopoul]

Hi to all,

Our treatment seems to lead to more intron retention because I can see signal in the intron sequences close to the exons.

Therefore, I plan to analyze the presence of splice variants in my RNA-seq data. There are many tools out there, but it seems that all of them are sophisticated and require a lot of work to be set up. I am looking for recommendations so I do not spend too much time playing around - before I find out :P

Preferentially I would like to have a tool that can quantify/ find intron variants (not exon based only)

Also, it would be great if the tools included good graphical output like sashimi plots.

I have already bookmarked the following packages.

SpliceWiz (looks very good so far) SUPPA2 LeafCutter bisbee spladder ASpli rMATS MAJIQ DEXSeq

Do you have any experience with these tools, and if yes, which would you recommend?

also, some tools are listed under this post, but it is already 7.5 yrs ago so maybe some better tools or updated tools are out there... Tools To Do the Alternative Splicing Analysis

EDIT: It would be great if this tool can differentiate between different splice variants for each gene (intron retention, exon skipping etc...)

Thanks for helping,

Nick

[iraun]

Hi! I personally use SplAdder, in case you want to add it to your list :).

[ntsopoul]

yes it looks like a good tool. Does it fulfill the criteria mentioned above?

1. quantify exon/intron?
2. have plot output (e.g. sashimi, volcano plot)?
3. does it differentiate between various splice variants for each gene (intron retention, exon skipping etc...)?

I do not see any plots in the documentation ...

Answer 1

[benformatics]

I would go with SUPPA2 or rMATS.

You can see some benchmarking here: https://www.nature.com/articles/s41467-023-36585-y