Hi, I'm wondering what exactly is the meaning of an aligner being "splice aware". I know it has to do with the mapping of reads spanning splice junctions, but as someone pretty new to RNA-seq and molecular biology, that's not quite enough for me to grasp the concept.
The following is my best reasoning of its meaning. RNA-seq reads are derived from mature mRNA, so there's typically no introns in the sequence. But aligners use a reference genome to aid in the process, so a read spans (what in the actual transcript are) two exons, while the reference would have one exon followed by an intron. So the reference genome would find a matching sequence in only one of the exons, while the rest of the read would not match the intron in the reference, so the read can't be properly aligned. A splice-aware aligner would know not to try to align RNA-seq reads to introns, and would somehow identify possible downstream exons and try to align to those instead, ignoring introns altogether.
Is this anywhere close to the meaning of splice-aware? And if so, would a splice-unaware aligner properly align RNA-seq data, given a reference transcriptome?