Monday, February 11, 2013

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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