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  • Shotgun Metagenomics data analysis

    Hi,

    I am new to shotgun metagenomics analysis. I have a project on the human gut microbiota. I know about MG-rast but I want to analyze my data by my own. I have done the quality checking and removal of host contaminated sequences. Now I want to check the taxonomical and functional profile of data. I have seen others use universal single copy marker genes reference. Where can I download these from?
    And What is the next step.

    Thanks

  • #2
    Originally posted by rozitaa View Post
    Hi,

    I am new to shotgun metagenomics analysis. I have a project on the human gut microbiota. I know about MG-rast but I want to analyze my data by my own. I have done the quality checking and removal of host contaminated sequences. Now I want to check the taxonomical and functional profile of data. I have seen others use universal single copy marker genes reference. Where can I download these from?
    And What is the next step.

    Thanks
    Have a look into:
    http://qiime.org/
    and
    http://www.mothur.org/

    Reference to databases:
    http://qiime.org/home_static/dataFiles.html

    This should get you started.

    Comment


    • #3
      Originally posted by fahmida View Post
      Have a look into:
      http://qiime.org/
      and
      http://www.mothur.org/

      Reference to databases:
      http://qiime.org/home_static/dataFiles.html

      This should get you started.
      Hi Thanks for quick answer. I have worked with Qiime before. But I mean shotgun sequencing not 16s rRNA analysis!

      Comment


      • #4
        you can use QIIME (even though it is on your own risk, as they state)

        http://qiime.org/tutorials/shotgun_analysis.html

        Comment


        • #5
          MEGAN might be one way to go, I haven't used it recently but the author seems to actively update it.

          There is a different approach here, too:
          Kraal, L., et al. (2014). "The prevalence of species and strains in the human microbiome: a resource for experimental efforts." PLoS ONE 9(5): e97279.

          Is the marker gene approach you are mentioning MetaPhlan? I don't know much about that.

          Comment


          • #6
            Cross-assembly, then taxonomic annotation (MEGAN or alike), gene calling, annotation, that should be the savest and easiest way to go.

            Comment

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