Figure 6: Examples of transcript calls and expression-level estimates.
From: Assessment of transcript reconstruction methods for RNA-seq
(a) The upper tracks show RNA-seq read coverage (from STAR alignments; see Online Methods) and annotated genes. Exon predictions from the ten methods that quantified transcripts are illustrated below the annotated gene by colored boxes. Exons predicted to belong to the same transcript isoform are connected. Original and median-scaled RPKM values are presented to the right and left, respectively, of the transcript models. For the gene RPF2, all methods reported different isoforms and expression levels. Where multiple overlapping isoforms were identified, that with the higher RPKM was selected for visualization, and spliced isoforms were prioritized over unspliced ones. The noncoding RNA U6 is not expressed. (b) Heat maps illustrate pairwise agreement between reported transcript isoforms for H. sapiens (left), D. melanogaster (center) and C. elegans (right). (c) Correlation between reported RPKM values and NanoString counts (Pearson r of log-transformed values). NanoString counts were compared to the highest RPKM value reported for transcript isoforms consistent with the probe design (correlation rc) or for any isoform from the locus (correlation ra).
