acids. Out of concern that some de novo assembled transcripts may be unannotated extensions of neighboring protein coding genes, as was recently observed for a fraction of GENCODE long noncoding RNAs [19], we created an additional filter to remove transcripts linked to neighboring genes by RNA-seq reads. To do this, we extended protein coding gene reference annotations using de novo transcriptome assembly and removed transcripts overlapping these extended gene structures (see Methods, Dataset S1).
