To select intergenic regions with high levels of expression that do not correspond to UTRs, we also calculated RPKM values for the 100 bp regions of the flanking genes closest to the intergenic regions. We selected those intergenic regions with the highest ratio of the RPKM value of the region of interest (within the intergenic region) to the RPKM of the start/stop of the flanking genes. We also looked for regions with a gap in expression between the gene and the region of interest. This will eliminate many regions that merely correspond to UTRs, and select for regions that are disproportionately expressed within the intergenic region only. We found this method to be most useful for selecting regions of interest, and successfully enriched our top hits for previously known small RNAs. The top 50 predicted RNAs can be viewed as a track in the GenomeView browser (see Supplementary  Information) .