rMATS: is there a way to quantify the utilization of each splice site?

[X L]

Hi All,

I know that rMATS is used to detect differential alternative splicing events from RNA-Seq data. However, if I want to quantify the utilization of each splice site based on RNA-Seq data, regardless of the event type, is there a way to extract this information from rMATS results?

Thanks,
Xiao

[kutsc...@gmail.com]

One way to get the read count for an individual splice junction is to run rMATS with --individual-counts. The additional output columns like upstream_to_target_count give the count for individual junctions. If the junction that you're interested in is part of a detected event then you can get the count that way. If an event with the splice junction isn't already in your output, you could use a --fixed-event-set that includes the junction in an event with a GeneID that has that junction annotated. You can also use --statoff to avoid any events being filtered out

Another option is to parse the .rmats files which are described in this post: https://github.com/Xinglab/rmats-turbo/issues/363
The last section of that file has counts of reads with different sequences of splice sites

Eric

[X L]

Hi Eric,

Thank you!

With the --individual-counts option, is the read count "normalized"? Additionally, is there a way to determine if the usage of each splice site (donor or acceptor) significantly increases or decreases between the two groups (Control vs. KO)? It’s similar to DESeq2, but in this case, we’re analyzing differential splice site utilization rather than differential gene expression.

Best regards,

Xiao

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[kutsc...@gmail.com]

The read counts are not normalized. I'm not sure what statistical test could be used for comparing the individual splice sites between the two groups

Eric

[X L]

Hi, Eric,

Thank you very much for your reply!

Best,

Xiao

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