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Old 11-09-2011, 07:19 AM   #1
Tube--
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Default 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!
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Old 11-09-2011, 08:04 AM   #2
Heisman
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You will probably like this thread: http://seqanswers.com/forums/showthr...uencing+manual
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Old 11-15-2011, 03:52 AM   #3
Tube--
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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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Old 11-15-2011, 04:23 AM   #4
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Old 11-15-2011, 05:05 AM   #5
GenoMax
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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).

Quote:
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?
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Old 11-30-2011, 08:41 AM   #6
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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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