Depends on intron length, scoring and possibly alternative location of the small exon. Hard to say without evaluation. I guess <20bp will be generally challenging for minimap2.

Can I change the scoring to somehow prioritize small exons?

A question for you @husamia. How does one know whether small exons are at all present in a newly sequenced and assembled (upto chromosomal level) genome? Will an ab-initio gene prediction software predict accurately a small exon?

Thanks
Abhijit

A question for you @husamia. How does one know whether small exons are at all present in a newly sequenced and assembled (upto chromosomal level) genome? Will an ab-initio gene prediction software predict accurately a small exon?

Thanks Abhijit

It depends on what you define to be your reference. You can find out if a small exon is missing from the assembly by experimentally sequencing the RNA transcripts and mapping it to the assembly. If you have extra RNA sequence not matching the DNA assembly there is chance that you have missing exon or novel exon.