> In addition to reducing the "the Minimum length of reas segments", do I also 
> need to reduce "Anchor length" to get more mapping on splicing junctins?

Definitely worth a try.

> Looks like the setting for "Anchor length" only affects the number of mapped 
> splicing junctions reported in the .splicing junctions output. Is my 
> understanding correct?

No, it will affect mapped reads as well.

> Does the "regions" mean the number of mapped splicing junctions?

Yes.

Best,
J.
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