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. 2012 Dec 18;41(4):e51. doi: 10.1093/nar/gks1311

Figure 1.

Figure 1.

Ambiguous split read resolved by TrueSight. A 75 bp read (SRR065504.21341241.2) from a human RNA-seq sample (detailed description in ‘Real datasets’ section) has two distinct splitting patterns, labeled in green and red. Mapping length on left and right side of both junctions is 11 and 64 bp, respectively. The same 11 bp sequence (orange) and donor splice site signal (red GT) exist in both gapped alignments. The junction shown in green has a higher TrueSight score (0.171) than the red junction (0.143) and supports a determination of exon skipping for gene KLC2, which is annotated by the UCSC Known Gene model (indicated by the green arrow on the left). MapSplice reported the junction shown in red and made an incorrect alignment for this read, whereas TopHat had not found an alignment for this read. Note that the gene model is for comparison only here, and was not used in TrueSight’s mapping procedure.