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Old 04-29-2009, 06:03 AM   #2
Location: Cambridge, MA

Join Date: Feb 2008
Posts: 82

You are correct that a true sequencing error can affect the interpretation of all downstream bases in _DNAspace_, however in colorspace, the bases would still show correct alignment to a colorspace reference. You would only see a 1nt mm. This is actually one of the reasons that colorspace can be useful outside of SNP detection. Depending on your application, alignment to a reference sequence in colorspace can allow you not only to detect the difference between a sequencing error (one nt mm in colorspace alignment) and a true SNP (a limited subset of specific _2nt_ mm in colorspace), but can also allow you to 'correct' a true sequencing error (again depending on your reference sequence and application) prior to decoding the sequence to DNAspace.
I would caution anyone against arbitrarily decoding CS to DNA prior to alignment. You are certainly going to introduce errors in DNA space that can cause spurious alignments. However, if you are simply counting tags, this is not necessarily a problem as long as you have a good estimate of background noise that a true signal should stand out against.
Long story short, it definitely depends on the application, but in most cases, if you can avoid immediately jumping to DNA space you will get the most out of your dataset.

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