RNA-seq analysis tools

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.

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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.