Fig. 6

Using simulated data to examine platform/aligner interaction. For each sequencing platform, all reads aligned by GSNAP, or STAR + Bowtie2 to Mup20 or Mup-ps22 from sample 9574 (untreated) were extracted. These data were re-aligned using STAR + Bowtie2 and the twelve most popular aligners, according to a survey of the literature. Additionally, simulated RNA-Seq reads were generated from both of these genes. Mup20 expression was simulated at three times the level of Mup-ps22. This figure displays the number of uniquely-mapped (top) and multimapped (bottom) reads aligned to Mup20 or Mup-ps22