Fig 1. Fragment start distributions modelled by Mix² model and Cufflinks.

(a) Set of eight β_ij. (b) Dashed curves: β_ijp(r|t = i, b = j). The p(r|t = i, b = j) are Gaussians equidistantly distributed along a 2000 bp transcript. Solid curve: p(r|t = i). (a) and (b) in transcript coordinates. (c), (d) Fragment distributions in locus with two transcripts, 1000 bp and 2000 bp long, sharing one junction. Long and short transcripts start 5000 bp and 5500 bp from beginning of locus contig. Junction starts at 6000 bp, extends to 6499 bp. Dashed curves: p(r|t = i) for Mix² model (c), Cufflinks (d), long and short transcript. Solid curve: p(r) for Mix² model (c), Cufflinks (d). (c) and (d) in genome coordinates.