FLOSS Bioinformatics Plugins
Geneious | CLC Genomics Workbench

Free/Libre/Open-Source Software for Microbial Research and Analysis.

Developed as part of project-based courses and volunteer work at the Boucher Lab (in the Department of Biological Sciences, University of Alberta).

RPKM Visualizer

RpkmVisualizer operates on the output of RNA-Seq to generate a circular bar graph of RPKM values for regions of a genome.

Links

Intended Use

The plugin is meant to be used as part of gene diversity and abundance analysis of microbial populations. The intended workflow involves assembling and annotating a consensus sequence from DNA reads from a sample of a population, and then using RNA-Seq on this sequence and the original set of DNA reads. Though RNA-Seq is normally purposed for gene expression analysis, it is used here for abundance analysis. Among the resulting table is a column RPKM, which stands for Reads Per Kilobase of exon model per Million mapped reads, and is a measure representing the amount of reads per annotated region (gene). The RPKM values can then be used to infer the relative frequency of the presence of genes in a population. RpkmVisualizer serves to represent these findings graphically by displaying the magnitude of the RPKM values for each region along the genome.