Furthermore, considering the reported prevalence of low level overlapping transcripts throughout intergenic sequence [7], it is not clear that full lincRNA structures can be unequivocally deconvoluted using short read RNA-seq technology. The determination of full lincRNA structures will be an important future effort in the field and may rely upon new datasets of longer read length and greater read depth, use of multiple orthogonal data types in the same tissue, new technologies such as ultra long read next generation sequencing, and further improvements in software for de novo transcript assembly.
