Workflow of ContextMap 2.(A) Reads are aligned to the reference sequence(s) using the integrated short read alignment program and the resulting alignments are classified into 4 different categories (top box, right side: full alignment, candidate single-split alignment, candidate multi-split alignment, and partial alignment). Dashed lines indicate unaligned sequence parts resulting from local alignments. Candidate single- and multi-split alignments are extended to split alignments using the sliding window approach (Figure 2). (B) Alignments less than d
apart are assigned to the same context. The maximum context size d
can be defined by the user (default is the average length of a mammalian mRNA). (C) Alignment extension of full (green box) and split alignments (see Additional file 1: Supplementary methods) to determine all valid alignments for a read. (D) + (E) Resolution of the best alignment for each read first within each context (D, local resolution) and then between all contexts (E, global resolution). For this purpose, a support score is calculated based on closely located alignments of other reads (bottom box, right side, and Additional file 1: Supplementary methods).