Figure 1From: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusionsTwo possible incorrect alignments of spliced reads. 1) A read extending a few bases into the flanking exon can be aligned to the intron instead of the exon. 2) A read spanning multiple exons from genes with processed pseudogene copies can be aligned to the pseudogene copies instead of the gene from which it originates.Back to article page