Quantile Normalization of RNA-Seq Reads. Box-and-whisker plots show median reads per gene (black and red bars) and varying ranges (colored boxes) for the lanes before normalization (A), which are removed after normalization (B). Red bars denote the lanes analyzed using updated RTA V1.6 software and therefore display an increase in total read counts per lane. Whiskers denote the lowest datum still within 1.5 interquartile range (IQR) of the lower quartile, and the highest datum still within 1.5 IQR of the upper quartile. Scatterplots of counts/gene between runs 2 and 3 in ABA-treated roots before (C) and after quantile normalization (D). A = ABA-treatment; P = PEG-treatment; H = H2O control; N = NaOH control.