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Old 12-05-2011, 12:36 AM   #1
kiradi
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Default 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
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Old 12-05-2011, 01:12 AM   #2
adamyao
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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
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Old 12-05-2011, 05:46 AM   #3
Heisman
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Is it whole exome data? Regardless, you might want to read through this thread: http://seqanswers.com/forums/showthr...uencing+manual
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Old 12-08-2011, 11:19 PM   #4
kiradi
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Quote:
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?
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Old 12-09-2011, 05:30 AM   #5
Heisman
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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.
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