Fig. 1
Landscape of RNA-Sequencing studies available in the Gene Expression Omnibus (GEO). (a) Since 2011, the number of RNA-Seq studies hosted in GEO has risen dramatically, from several hundred to over 10,000, well eclipsing the number of microarray expression studies currently produced per year. (b) While small relative to the total set of RNA-Seq studies in GEO, there is a substantial number of RNA-Seq studies available for the CF pathogen species featured in the CF-Seq application. (c) To derive meaningful biological insights from the RNA-seq studies in GEO, the analysis pipeline outlined here must be followed. Alignment of sample RNA sequences to a reference genome is accomplished with a command line tool like SALMON, and downstream analysis with a tool such as the popular R package edgeR. CF-Seq automates the second segment of this pipeline, saving users from the need to clean up count tables, produce experimental design matrices, gather metadata, and write sophisticated analysis code in R.
