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  • xuguorong
    Member
    • Feb 2010
    • 27
    #1

    SAMMate 2.5

    All-new SAMMate 2.5 is released.

    RNA-Seq Transcript De novo Assembly and Quantification using SAMMate
    http://sammate.sourceforge.net/
    RNA-Seq assembly and analysis


    New features:
    RAEM-Read Assignment via EM (Deng et al. 2011, Nucleic Acids Research, doi: 10.1093/nar/gkr042)
    One-step iQuant (isoform Quantification, manuscript in preparation)
    Iterative iQuant (isoform Quantification, manuscript in preparation)
    Output read counts for detecting differentially expressed genes and differentially expressed transcripts. e.g. using edgeR
    Last edited by xuguorong; 04-08-2011, 01:47 PM.
    Tags: None
  • questioner
    Junior Member
    • Jun 2009
    • 6
    #2
    How long (approximately) does it take to quantify a transcriptome profiled with 15 million reads at isoform-level?

    Comment

    • tonge
      Junior Member
      • Mar 2011
      • 5
      #3
      @ Xuguorong,
      I haven't been able to find any information regarding small RNA deep sequencing and Sammate. Sammate looks very user friendly but I am wondering - Is sammate suitable for processing BAM files derived from a miRNA reads? and if so, what type of annotated track is best for visualising my miRNA data on sammate?
      Thanks

      Comment

      • xuguorong
        Member
        • Feb 2010
        • 27
        #4
        Hi tonge,

        The current functionalities are focused on mRNA isoform quantification and microRNA quantification would be released soon.

        Thank you for using SAMMate!
        Guorong

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