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Old 06-01-2012, 06:27 PM   #1
lg36
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Location: london

Join Date: Mar 2012
Posts: 12
Default Which Pipeline is Correct??

Dear All,

I'd be very grateful for any advice on which (if any) of the following processes to take for SNP discovery? I find a different number of SNPs with each approach with the same SNP filters applied throughout.

Raw FastQ File --> Direct Mapping to Reference --> SNP discovered 1,200

Raw FastQ File --> De Novo Assembly --> Extract Paired Contigs --> Map Paired Contigs to Reference --> SNPs discovered 1,089

Raw FastQ File --> De Novo Assembly --> Extract All Contigs --> Map Contigs to Reference --> SNPs discovered 1,383

How can I know which SNPs are correct. Would it be useful to test the quality of the corresponding consensus sequence (for sets of known nucleotides?) or would that not help to judge which is most accurate.

Best wishes lg36
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