Figure 2. Venn diagrams comparing differentially expressed transcripts (DETs) between the Nrl^−/− and WT groups from BWA and TopHat analyses. Despite major differences in the UCSC refFlat annotations used by Burrows-Wheeler Aligner (BWA) and Ensembl annotations used by TopHat, most of the genes identified by BWA were also identified as significant by TopHat. A: Comparison of the total number of DETs identified as significant (fold change ≥1.5 and p-value <0.05) by the two methods. B: Inclusion of the top 500 DETs (424 unique genes) identified as significant by BWA and in the full TopHat DET list. C: Inclusion of the top 200 DETs (179 unique genes) identified as significant by BWA and in the full TopHat DET list. We assess the two methods based on a comparison of qRT–PCR data for the genes detected by either or both methods. The discrepancy between the results can be attributed to differences in the input annotation files used (UCSC refFlat versus Ensembl GTF) by the two methods and their alignment algorithms.