Mapping and downstream analysis of RNA-seq data. (a) Total number of RNA-seq reads mapped to exonic, junction, intronic and intergenic regions as well as the fraction of mapped reads for all four samples. Pie charts below visualize the distribution of all mapped reads. (b) An example of an output from the pipeline, visualized in the UCSC genome browser, showing the Upf2 gene locus, with junctions supported by reads (horizontal bars in each sub-window), and exon coverage (vertical bars). Refer to Figure S1 in Additional file 2 for another example of a genome browser output. No minimum read cutoff was used for junction visualization. The very low exon coverage present for knocked out exons 2 and 3 in KO samples represents a miniscule amount of non-recombined tissue/cells.