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  • which aligner can try?

    hi everyone,

    I want to align my RNA-seq data to a cDNA reference and I want to find where does the SNP occur. which aligner suit for me to try it??
    Can someone give me some suggestion??
    Many thanks for help!!


    Sincerely, Eric

  • #2
    Some basic information here: http://en.wikibooks.org/wiki/Next_Ge..._%28NGS%29/RNA

    A practical guide about how to do this using TopHat: http://www.nature.com/nprot/journal/....2012.016.html

    STAR is not mentioned in the first guide but is a fast aligner for RNA-seq data: http://code.google.com/p/rna-star/

    Evaluation of RNA-seq alignment algorithms: http://www.plosone.org/article/info%...l.pone.0052403

    For calling SNP with RNA-seq data you are likely to need pretty deep coverage (> 50 x).
    Last edited by GenoMax; 07-09-2013, 03:17 AM.

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    • #3
      If you are aligning to cDNA you don't need anything fancy, like topHat, because your reads will not be spliced compared to your reference. You can use bwa, or bowtie, or whatever.

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      • #4
        Another aligner you may try is the subjunc aligner included in Subread package (http://subread.sourceforge.net)

        Best wishes,

        Wei

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        • #5
          many thanks for helping me

          Dear all above,


          thanks for your helpful answers, I will try those you supplied


          Sincerely,

          Eric

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