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-   -   Help to analyze Illumina HiSeq 2000 Human data (http://seqanswers.com/forums/showthread.php?t=16007)

kiradi 12-05-2011 12:36 AM

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

adamyao 12-05-2011 01:12 AM

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

Heisman 12-05-2011 05:46 AM

Is it whole exome data? Regardless, you might want to read through this thread: http://seqanswers.com/forums/showthr...uencing+manual

kiradi 12-08-2011 11:19 PM

Quote:

Originally Posted by Heisman (Post 58720)
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?

Heisman 12-09-2011 05:30 AM

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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