Fig. 1

slncky sensitively filters lncRNAs from reconstructed RNA-Seq data. a Schematic of slncky’s filtering pipeline. Annotated coding genes are shown in dark gray, reconstructed transcripts in medium gray, and filtered transcripts in light gray. b Histogram of log₁₀(P values) of coding potential as evaluated by RNACode (Washietl et al. [18]) for slncky-identified lncRNAs (gray) and coding genes (red). c Scatterplot of log₁₀(P-values) of coding potential (x-axis) and log₁₀(ribosomal-release scores) (y-axis) of slncky-identified lncRNAs (gray) and coding genes (red). Distributions of ribosomal-release scores (RRS) are displayed along right side of y-axis. Dotted lines denote one standard deviation above and below the mean of RRS distributions. slncky-identified lncRNAs have significantly higher coding potential P-values and lower RRS than coding genes. d Comparison of previously published sets of lncRNAs to slncky results. Number of transcripts also annotated as a lncRNA by slncky (gray), number removed by slncky as gene duplication or coding (light and dark blue), and number of additional transcripts annotated as a lncRNA by slncky but not the previous pipeline (purple). e Percentage of well-characterized lncRNAs identified in previously published sets compared to slncky results. Numbers above bars denote absolute number of lncRNAs