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  • kiradi
    Junior Member
    • Dec 2011
    • 2
    #1

    Help to analyze Illumina HiSeq 2000 Human data

    Dear List,

    I am new to NGS field. I have paired end sequenced Human Illumina HiSeq 2000 Data and have find SNP's out of that. And then I have to fidn out association of SNP's to a perticular trait. I would like to use open source tools such as bioconductor packages for data analysis. Hence, can somebody give me a functional pipeline for data analysis?

    Thanking you in anticipation.

    Regards,
    Kiradi
    Tags: None
  • adamyao
    Member
    • Feb 2011
    • 18
    #2
    Dear kiradi,

    You can try VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do) to see if it helps. It provides MegaQuery Download to download millions of annotated variants for NGS data in minutes.

    Adam

    Comment

    • Heisman
      Senior Member
      • Dec 2010
      • 534
      #3
      Is it whole exome data? Regardless, you might want to read through this thread: http://seqanswers.com/forums/showthr...uencing+manual

      Comment

      • kiradi
        Junior Member
        • Dec 2011
        • 2
        #4
        Originally posted by Heisman View Post
        Is it whole exome data? Regardless, you might want to read through this thread: http://seqanswers.com/forums/showthr...uencing+manual
        Yes it is whole Exome data. I have gone through your documentation. it was really good. May I know is there any something similar packages available from bioconductor?

        Comment

        • Heisman
          Senior Member
          • Dec 2010
          • 534
          #5
          It's not my documentation, haha.

          A lot of those things are available freely to anybody. For example, type in "donwload GATK" into google and you'll find the right link.

          Comment

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