Finding the right reference sequence for RNA-Seq

For prokaryotes, the reference sequence needed for RNA-Seq is quite simple. Either you input a genome annotated with gene annotations, or you input a list of genes and select the Use reference without annotations.

For eukaryotes, it is more complex because the Workbench needs to know the intron-exon structure as explained in the introduction. This means that you need to have a reference genome with annotations of type mRNA and gene (you can see the annotations of a sequence by opening the annotation table). You can obtain an annotated reference sequence in different ways:

Image downloadhumangenome
Figure 27.6: Downloading the human genome from refseq.