Detecting genes that are differentially expressed between conditions is a fundamental part of understanding the molecular basis of phenotypic variation. To take advantage of the possibilities and address the challenges posed by this relatively new type of data, Blast2GO offers several tools to analyze RNA-seq data and obtain functional insights.

Figure 1: RNA-seq options

The rna-seq option in Blast2GO provides an easy and fast way to:

  1. Reconstruct the transcriptome from RNA sequencing data, assembling short nucleotide sequences into longer ones without the use of a reference genome. This functionality is based on Trinity
  2. Quantify gene and isoform expression levels from RNA-Seq data. The algorithms used for this purpose is inspired by the well-known HTSeq and RSEM software packages . 
  3. Perform a differential expression analysis of expression data to find differentially expressed genes between experimental conditions or over time. This functionality is based on two Bioconductor popular packages, edgeR and maSigPro, which are executed via the Blast2GO Service Cloud.