EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes

Question

[buthercup_ch]

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-estimated-degree-of-gene-expression-in-prokaryotic-genomes-article-a3586-abstract http://ccb.jhu.edu/software/EDGE-pro/

Does anyone experience with this one?

Thanks in advance for help

Answer 1

[zh.khodadadi]

Hi I have the same question.Do you understand ?

Answer 2

[colindaven]

I do not have experience with EDGE-pro, but Rockhopper seems to be pretty good as an alternative

http://cs.wellesley.edu/~btjaden/Rockhopper/

Answer 3

[zh.khodadadi]

Hi I have a question why I dont use Tuxedo pipeline for bacteria?(Cufflinks,cuffmerge,Cuffdiff)

[zh.khodadadi]

Does cuffmerge use for bacteria?

[GenoMax]

If you are following tuxedo pipeline then yes. But as we have been over this in other threads (you started) why you would want to use it for bacteria (where splicing is not a feature you need to worry about) is the question.

[zh.khodadadi]

I wanted to compare some pipeline for my rna seq data(Differential expression of genes for bacteria). do you introduce me some paper/article that I Get to know all pipeline that analyze the Prokaryotes rna seq and stage of bacteria pipeline(after align why we do counting with HTseq and how to do Differential expression analysis edgeR ).I mean The main concepts.I am familiar to tuxedo pipeline. thanks.