Fig. 2

Overview of the method, on an example. a: A toy configuration, with three genes in black: A, B, and C. Notice that A and B overlap. Six reads have been mapped to the genome, some of them (reads 2, 4, and 6) map at two different locations. If a read maps unambiguously to a unique locus and matches a unique gene (like read 1), we attribute the corresponding gene to the read (here, gene A). If a read, like read 2, matches two different genes, we create a “merged” gene, here A–C, and attribute this merged gene to the read. If a read (read 3) does not match any gene, it is not used. If a read (read 4) matches a gene (gene A) and an intergenic region, the read is attributed to the gene only. If a read (read 5) matches two different genes because the genes overlap, the read is also attributed to the merged gene (gene A–B). Similarly, if a read (read 6) matches two overlapping genes and an other gene, the three genes are merged (A–B–C). Table b provides the attributed gene for each read. c is the quantification table and the output of the tool for this configuration. Genes are sorted in lexicographical order, as shown in the example. As a consequence, merged gene (A, B) will always be displayed as A–B, and never as B–A