FlyBase RNA-Seq RPKM data calculations available for bulk download


FlyBase is extending its initial gene-level analyses of RNA-seq throughput data from modENCODE and others. The algorithm for RPKM (reads per kilobase per million mapped reads) has been refined, additional datasets have been analyzed, and these data are now available for bulk download.

In order to summarize this type of data at the gene level, it is necessary first to determine a single value for the expression level of each gene for each RNA-seq sample. RNA-seq coverage data are intersected with FlyBase exons, based on the gene model annotations of the current release, to calculate a single value reflecting average coverage per kb per gene. Each gene data point is then classified into one of eight expression level bins, and the graphical and text summaries were produced from the binned values. A more detailed explanation may be found at FBrf0221009.

Bulk data files can be accessed from the Precomputed Data Files page (menu: Files → Current Release). Look in the Genes section; the item line is ‘RNA-Seq RPKM values’. You can download the file directly by clicking here.

Simple and combinatorial queries of RPKM expression data can conducted using the ‘RNA-Seq Search’ option found under the ‘Expression’ tab in the Quick Search tool.

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