Further description of these PET clusters, including how the annotations were generated, is available at the UCSC Genome Browser site here http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=321010719&c=chr21&g=wgEncodeGisRnaPet. BEDTools was employed to compute overlap between lincRNA and RefSeq NM gene 5′ and 3′ ends and PET cluster 5′ and 3′ end ‘blocks’. In the case of ambiguous stranded lincRNAs, both potential orientations were allowed for determining overlap with the 5′ and 3′ ends of PET clusters.
