Despite the fact that most previously annotated noncoding RNAs failed to pass our filters, our lincRNA catalog contains significantly more lincRNAs than previously known (>94% of lincRNAs are entirely novel at each expression level). This is the result of two unique features of our study. First, the RNA-seq read depth and diversity of tissues surveyed allowed for the detection of rare and tissue specific transcripts that were previously unknown. Many of these novel transcripts passed all filters and are annotated as novel lincRNAs in our catalog. Second, in contrast to prior lincRNA annotation efforts that were restricted to identification of only spliced or polyadenylated lincRNAs [16], [19], [41], we sought to generate annotations of a more complete set of human lincRNAs regardless of splicing or polyadenylation status. The reasons for taking this approach are manifold. Two of the most well known and abundant functional human lincRNAs, NEAT1 and MALAT1, are single exon genes (as are approximately 5% of protein coding genes) [42], suggesting that non-spliced transcripts may make up an important class of lincRNA. Additionally, numerous functional nonpolyadenylated noncoding RNAs
