see here http://allaboutbioinfo.blogspot.com/
Which tool is used for RNA-seq analysis?
Which tool is popular to perform RNA-seq analysis, including read mapping, gene/transcript expression level estimation and differential analysis? Here is the survey of which tool to used for RNA-seq analysis.
In summary, the majority will:
- aligns the reads to the genome (or genome+transcriptome) using Tophat;
- count reads using Cufflinks (the second choice is HTSeq-count, which is becoming popular);
- perform differential expression using DESeq/DEXSeq (followed by CuffDiff);
- use Ensemble (followed by Refseq/UCSC) as the annotation resource;
- use GOSeq (followed by IPA and Genego Metacore) for downstream analysis.
update 07/16/13
several packages have been developed to simplify(automate) the process:
blacktie http://xguse.github.io/blacktie/index.html
Nesoni http://www.vicbioinformatics.com/software.nesoni.shtml
I will give Nesoni a try in the near future, it use limma to detect the differentially expressed genes which I like very much, but I have to let the HPC center install it first. RNA-seq
data are just too big, I can not run the analysis on my own computer, especially when I have multiple replicates.