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Old 05-04-2010, 04:47 AM   #1
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Location: Graz, Austria

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Default Targeted sequencing


we are planning to do targeted resequencing for genetic diagnostics in our laboratory using the FLX instrument with titanium chemistry.
I now wonder if I should align the results (we do not have results yet, only theory) against the whole human genome or if it's enough to align against the targeted genes?
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Old 05-04-2010, 06:15 AM   #2
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We usually align against the genome since with Agilent whole exome sequence selection you get ~100 bp of flanking intron sequence. You can detect mutations affecting splicing by including the intron sequence in your alignment.
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