Individual Counts

[bmwx410]

Hi,

Thank you for the tool.

I am trying to do batch correction on the junction reads, and am trying to extract the categorised junction supporting reads.
Hence trying to understand how rMATS works a little more.

Why does the individual counts supporting IJCs or SJCs often not add up to the total value.

i.e.

Upstream_to_target and target_to_downstream are the read categories I presume support IJC so why does their total not equal the IJC.

I presume therefore that these are separate to the computation of the IJC and some other processing goes on with other counts?

Some help understanding this would be greatly appreciated!

Thanks

[EricKutschera]

It's possible for an alignment to cover both the upstream_to_target junction and the target_to_downstream junction if the alignment covers the entire target exon. In that case the alignment is counted only once for the IJC column

Here's a related post: https://groups.google.com/g/rmats-user-group/c/My1xSMj_t3k/m/knnQfkdgAAAJ