<p>HMMSplicer discovers the non-canonical <i>XBP1</i> intron. HMMSplicer identifies three reads containing the non-canonical CA-AG splice site in <i>XBP1</i>. Because the reads are fairly evenly split, both read-halves aligned to the genome. The edges identified by HMMSplicer are 2 and 4 bp off from the actual splice site because the sequence at the beginning of the intron repeats the sequence at the beginning of the subsequent exon. When identical junctions are collapsed, there are two junctions, one with a score of 1024 and one with a score of 1030, which puts them in the top 0.5% of the collapsed non-canonical junctions.</p
