RNA-Seq data optimization strategy. The flowchart outlines the strategy for identifying soybean leaf transcripts significantly changing in response to elevated ozone. All genes mapping zero reads for all samples were removed (A) after aligning raw reads to the reference transcriptome, consisting of 46,367 genes. Differential expression was then separately determined using DESeq and edgeR (B). The two lists of significant genes were intersected to obtain a single list of differentially expressed genes (C). Finally, low expression genes (RPKM < 1.0) were removed (D).
Yendrek et al. BMC Research Notes 2012 5:506 doi:10.1186/1756-0500-5-506