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  • Info on analyzing exome sequencing data

    Hello! I'm a med student doing some research. I would need to analyze data, which came from exome analysis. I'm a real beginner with that. Do you guys know any good internet tutorials on exome sequencing in general and on analyzing the data that comes out of it? I mean real beginner things, I read the Wikipedia article on exome sequencing, it was way above my comprehension level. They don't really teach these thing on med school.

    Thanks!

  • #2
    You will probably like this thread: http://seqanswers.com/forums/showthr...uencing+manual

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    • #3
      Thanks, I read briefly through it, but it seems that my data has already gone through those steps. I have an excel file that contains all the SNPs that were found. Now I should filter that SNP data somehow, to discover SNPs that are meaningful. The guys in the biotech lab used these tools:
      SOLiD LifeScope software v. 2.1 (hg19)
      Agilent Human hg19 all exon 50Mb kit target annotations

      So now I have the SNP file in excel format that I should filter. Any ideas on how to start?

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      • #4

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        • #5
          Sounds like you want to map your SNP's to genes and go forward from there.

          Look at this thread on biostar: http://biostar.stackexchange.com/que...ne-around-60kb

          You can also use the BioMart tool in Ensembl (http://www.ensembl.org/Homo_sapiens/Info/Index) to do this (http://www.biomart.org/).

          Depending on how many SNP's you have a simple search could be done this way: https://lists.soe.ucsc.edu/pipermail...ry/025082.html
          You can also use the "table browser" from UCSC site to do lookups on multiple SNP's (http://genome.ucsc.edu/goldenPath/he...ablesHelp.html).

          Originally posted by Tube-- View Post
          Thanks, I read briefly through it, but it seems that my data has already gone through those steps. I have an excel file that contains all the SNPs that were found. Now I should filter that SNP data somehow, to discover SNPs that are meaningful. The guys in the biotech lab used these tools:
          SOLiD LifeScope software v. 2.1 (hg19)
          Agilent Human hg19 all exon 50Mb kit target annotations

          So now I have the SNP file in excel format that I should filter. Any ideas on how to start?

          Comment


          • #6
            Tube--, it depends on the model of you disease and the data you have available. Are you looking at a recessive disease ? Is there consanguinity in the patients' family ? Is this a multiple patient cohort ? Do you have controls ? Are there any trios (father, mother, affected child) ?

            As raonyguimaraes already showed, there are common steps one can use to filter out uninteresting SNPs. There are many ways to do so, raonyguimaraes show a pipeline that is commonly used. If you give us more details on the model of the disease and the actual data you have we'll be in a better standing to help you.

            Simon

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