Fig. 3
Ambiguous reads resolution. a: The read is included in both genes A and B. Here, the resolution cannot be solved, and the read will be attributed to gene A–B. b: The read is not totally included in gene A, neither in gene B. n A nucleotides of the read overlap with gene A, and n B overlap with gene B, and n A >n B . If n A ≫n B , we may attribute the read to gene A only. However, if n A ≈n B , the ambiguity cannot be resolved, and the read is attributed to A–B. The two following cases show the rules to resolve ambiguity. c: We suppose here that n A >n B +N, where N is a parameter set by the user (default: 30). In this case, mmquant will attribute the read to gene A only. d: We suppose here that n A >n B ×P, where P is given by the user (default: 2). The read will be attributed uniquely to gene A. e: Here, the single end read contains an intron. Exon-wise, the read can be attributed to gene A or B. In case of ambiguity, introns are compared. The intron of the read matches the intron of gene A, whereas gene B has no intron there. The read is thus attributed to A. f: The read is ambiguous exon-wise. We compute nA′ and nB′, the number of nucleotides shared by the intron of the read and the introns of genes A and B respectively. Ambiguity is solved using nA′, nB′ and the rules given in c and d. g: The read is paired-end. In case of ambiguity, n A and n B are computed as the sums of the overlapping bases between the two reads and the gene A and B respectively. The rules presented in c and d apply next