Due to inherent limitations of de novo transcriptome assembly using short reads of finite depth, it is not always possible to unequivocally determine the complete structure of a transcript. This is particularly true for lowly expressed transcripts where the number of reads available is limited, and for genomic regions to which reads cannot be uniquely mapped. In the case of shallow read depth, exons of multi-exonic transcripts may lack reads connecting the exons, and de novo assembly could result in separate annotation of each exon as a distinct transcript. In support of this, we found that lower expressed lincRNAs discovered from de novo transcript assembly were less likely to have multi-exonic structures (Table S5). Additionally, the annotated 5′ and 3′ ends of the lincRNAs may represent truncations of the full length transcripts. Indeed, our analysis of PET tag data revealed that while the majority of our lincRNA catalog is overlapped by at least one PET tag, in most cases there is minimal PET tag support for the annotated 5′ and 3′ ends of the lincRNAs (Table S6). It is therefore
