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 have been described [30], [43]. Even long noncoding RNAs which can be spliced are often found in their unprocessed forms [44], a distinct property of long noncoding RNAs that would result in missed lincRNAs if splicing were a required attribute. Therefore, we chose not to exclude any lincRNAs from this catalog due to lack of splicing or polyadenylation. Importantly, because nonspliced, nonpolyadenylated transcripts could theoretically be erroneously de novo assembled from reads derived from contaminating genomic DNA in RNA-seq data, we took multiple measures to mitigate any contributions of genomic DNA contaminant reads (see Methods).
