Fig. 4

Main output files from SPEAQeasy. SPEAQeasy produces the files described in the blue boxes, as the final products of interest. Counts of genes, exons, and exon-exon junctions are aggregated into three respective R objects of the familiar RangedSummarizedExperiment class. This allows users to immediately follow up with a number of Bioconductor tools to perform any desired differential expression analyses. If the --coverage option is provided, RData files are produced to provide expression information over regions in the genome. This allows users to compute differentially expressed regions using any of a number of Bioconductor packages as appropriate for the experiment. Finally, for experiments on human samples, variants are called to ultimately produce a single VCF file of genotype calls at 740 particular SNVs. Together with genotype data recorded before sequencing the samples, one can resolve mislabellings and other identity issues which inevitably occur during the sequencing process (http://research.libd.org/SPEAQeasy-example)