Figure 2

Detection of single-split and multi-split alignments in ContextMap 2.(A) Detection of single-split alignments as part of step 1. First, reads are aligned to the genome and candidate split alignments (A ₁) are identified. Second, reads with candidate split alignments are re-aligned within a window around the initial alignment to determine a completing alignment (A ₂). The use of smaller seed lengths than in the initial alignment allows recovering completing alignments shorter than the seed length used for the initial alignment. Finally, the alignments are combined to a complete split alignment. (B) Detection of multi-split alignments. For every candidate multi-split alignment, ContextMap 2 creates two fragments of the respective read sequence (i.e. f ₁ and f ₂ for A ₁ and f ₃ and f ₄ for A ₂). Subsequently, single-split alignments are detected for these fragments. Finally, overlaps of single-split alignments are combined to obtain a complete multi-split alignment after first identifying the best splice site for each split alignment as part of the resolution of overlapping splice sites in step 4 of ContextMap 2.