Tweet
Hello,
We are studying the differential gene expression of bacteria under different growth conditions, by applying RNA-Seq.
The pipeline she used so far is the following:
- After quality check and trimming by using Trimmomatic, we use TopHat for mapping the reads against the bacterial genome, and then we use Cufflinks (Cuffdiff) for the analysis of differential expression.
My question is the following, as TopHat has been designed to detect exon-exon junctions in eukaryotic genomes, how this will affect the analysis of a prokaryotic genome?
I just found information about what seems to be an alternative to TopHat when dealing with bacteria, that is EDGE-pro: http://www.la-press.com/edge-pro-est...a3586-abstract
Does anyone experience with this one?
Thanks in advance for help
We are studying the differential gene expression of bacteria under different growth conditions, by applying RNA-Seq.
The pipeline she used so far is the following:
- After quality check and trimming by using Trimmomatic, we use TopHat for mapping the reads against the bacterial genome, and then we use Cufflinks (Cuffdiff) for the analysis of differential expression.
My question is the following, as TopHat has been designed to detect exon-exon junctions in eukaryotic genomes, how this will affect the analysis of a prokaryotic genome?
I just found information about what seems to be an alternative to TopHat when dealing with bacteria, that is EDGE-pro: http://www.la-press.com/edge-pro-est...a3586-abstract
Does anyone experience with this one?
Thanks in advance for help