Help to analyze Illumina HiSeq 2000 Human data

kiradi · 12-05-2011, 12:36 AM

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

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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12-05-2011, 12:36 AM	#1
kiradi Junior Member Location: India Join Date: Dec 2011 Posts: 2	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

12-05-2011, 01:12 AM	#2
adamyao Member Location: Taiwan Join Date: Feb 2011 Posts: 19	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

12-05-2011, 05:46 AM	#3
Heisman Senior Member Location: St. Louis Join Date: Dec 2010 Posts: 535	Is it whole exome data? Regardless, you might want to read through this thread: http://seqanswers.com/forums/showthr...uencing+manual

12-09-2011, 05:30 AM	#5
Heisman Senior Member Location: St. Louis Join Date: Dec 2010 Posts: 535	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.