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SNPs analysis

SNP analysis bioinformatics

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#1 Lj Lee

Lj Lee

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Posted 30 June 2014 - 10:54 PM

I have done part of the bioinformatics analysis of my Illumina HiSeq DNA-seq data, all of them were filtered, aligned and SNPs were called out. I'm using AVADIS NGS software to do all the analysis. Now I get a lot of output data(all the SNPs) from my different 3 groups of subject. Any idea on what kind of downstream analysis I can do to compare within these 3 groups? I get quite a number of known and novel SNPs from all these 3 groups. A bit confusing on what to do next as I'm still new in this. 

 

Many thanks. biggrin.png



#2 jerryshelly1

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Posted 01 July 2014 - 07:22 AM

You could either organize them into groups or just analyze them separately. Feed your results into SeattleSeq and it will return you a spreadsheet that gives the standard dbSNP information. From there, you can compare the frequencies within the population and determine which SNPs are novel







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