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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:

    and
    The website that supports the mothur software program - one of the most widely used tools for analyzing 16S rRNA gene sequence data. Step inside to learn how to use the software, get help, and join our community!


    Reference to databases:


    This should get you started.

    Comment


    • #3
      Originally posted by fahmida View Post
      Have a look into:

      and
      The website that supports the mothur software program - one of the most widely used tools for analyzing 16S rRNA gene sequence data. Step inside to learn how to use the software, get help, and join our community!


      Reference to databases:


      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)

        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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