Fig. 4

A genome-based transcript map showing misassembled Trinity contigs (purple track) and improvements made by FRAMA’s mRNA boundary clipping (red track). Human RefSeq counterparts to FRAMA transcripts are shown in green. Trinity provides a plethora of (putative) transcript isoforms (63 contigs) for the HYAL1-NAT6-HYAL3 locus, many of them being read-through variants that join neighboring genes (informative subset in purple track). Although FRAMA is not able to resolve the shared first exon of the NAT6-HYAL3 locus correctly, mRNA boundary clipping improved the raw assembly substantially by separating the gene loci. Genome-based methods (brown tracks) struggle in predicting the correct gene loci, too: TKIM shows the best performance, separating each gene locus correctly. GENSCAN correctly separates HYAL1, NAT6 and HYAL3 loci, but joins neighboring loci (HYAL1 with HYAL2 and HYAL3 with IFRD2). GNOMON correctly provides several different HYAL3 variants, but misses NAT6 completely. Throughout the figure, thick bars represent coding regions, thin bars untranslated regions and lines introns. Arrows on lines or bars indicate the direction of transcription. Accession numbers of external gene models are listed in Additional file 1: Table S11