FIGURE 5.

ShortStack annotates diverse types of small RNA genes. (A) Cumulative fraction of all col_leaf small RNA genes with a DicerCall of 21 that were subjected to phasing analysis, ranked by adjusted P-value. The ShortStack-generated P-values were adjusted using the Benjamini-Hochberg procedure to control for the false discovery rate (FDR) during multiple testing; the dotted line indicates an FDR of 0.05. Points in red represent ShortStack clusters that overlap a list of Arabidopsis loci previously described to produce phased small RNAs. (B) As in A, for the col_aerial data set. (C) As in A, for the tomato data set, using a list of tomato loci previously described as producing phased small RNAs. (D) Scatterplot of hairpin length as a function of small RNA abundance for all loci annotated as hairpin-associated (HP) from the col_leaf data set. Dotted lines indicate cutoffs for long hairpins (>500 nt) and highly abundant (>100 reads per million). Two known loci, IR71 and IR2039, are labeled. This ShortStack analysis increased the value of option --pad from the default value of 100 to 300. (E) As in D, except for the col_aerial data set. (F) ShortStack-annotated small RNA genes from the fly_ovary analysis that overlap a set of known endo-siRNA loci from Drosophila ovaries, grouped by DicerCall and secondary structure. (G) As in F, except for a set of known Drosophila piRNA loci. (H) As in F, except for the mouse_testes analysis with respect to a set of previously described murine piRNA loci. (I) ShortStack-generated polarity assignments for small RNA genes overlapping previously annotated sets of piRNA loci from Drosophila and mouse. (ds) Double-stranded.