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  • #1

    RNA-Seq software evaluation?

    Hi,everyone
    I am recently focusing on the RNA-Seq analysis. I want to know the performances of some softwares in this section, such as alignment, assembly, expression, SNP, and so on. Can you provide some suggestions or reference materials?
    Thank you
    Tags: None
  • #2
    I really need your help, please give me some suggestions. Thanks

    Comment

    • #3
      Unfortunatelly there is no comprehensve review/comparison.
      You have to go through many papers to figue out what is going on in the field.

      You can start by analysing the papers cited in this review:
      Ozsolak F, Milos PM. (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genetics 12, 87-98.
      Pawel Labaj

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      • #4
        also interesting:
        Synthetic spike-in standards for RNA-seq experiments - PubMed
        http://www.ncbi.nlm.nih.gov/pubmed/21816910
        High-throughput sequencing of cDNA (RNA-seq) is a widely deployed transcriptome profiling and annotation technique, but questions about the performance of different protocols and platforms remain. We used a newly developed pool of 96 synthetic RNAs with various lengths, and GC content covering a 2(2 …

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        • #5
          and the m erging section of the How to WIKI :-)
          SEQanswers
          http://seqanswers.com/wiki/How-to

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