What is the diff between spliced alignment and ungapped alignment?

[arkilis]

Joined a workshop recently. They are talking about the RNA Seq which is not my territory. Lack of knowledge on this field.

So any diff between those two? Thanks

[vivek_]

Splice aware aligners take into account the splice junctions between exons in gene regions while aligning RNA-seq reads. So if a read spans the splice junction on either side, it gets aligned as such.

In ungapped alignment, the splice junction would indicate only a partial match for the reads that span these junctions and it might not be aligned.