Theoretical estimation of quantifiable splice junctions in relation to read depth and read length. Subsampling of an RNA-seq sample in HEK293 cells, originally containing 380 M reads with a read length of 150 nt, is used to estimate the number of introns spanned by at least 10 reads, which we denote as quantifiable splice junctions. (A) The number of quantifiable splice junctions is shown in a heat map (color scale from dark purple—0—to yellow—1 M—quantifiable splice junctions) by read length (rows) and read depth (columns). Green box denotes ENCODE standard library characteristics resulting in ∼600,000 quantifiable splice junctions, and gray box denotes alternative selections of read length and read depth, resulting in a similar number. (B) Possible combinations of read length and read depth are displayed that result in 600,000 (pink), 700,000 (magenta), or 800,000 (purple) quantifiable splice junctions.
