Identifying conserved transcripts

After creating the lncRNA catalogues we used LiftOver to evaluate orthologous regions between the primate species. Based on the validation from TE LiftOver we again used 0.1 for the minimum ratio of bases that must remap. The conservation of lncRNAs was done based on our human annotation. We lifted lncRNAs from human to each of the 3 NHPs. We then performed expression analysis in non-human primates on the LiftOver lncRNAs to determine which are also expressed in NHP. RPKM values were calculated for each transcript using the Bioconductor package Rsubread. Reads were counted using featureCounts(), and normalized using rpkm() [56]. Expressed transcripts are defined as those with 1 RPKM or greater. For species with biological replicates this cutoff was required in all replicates to be deemed expressed.