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Old 12-05-2009, 08:00 AM   #36
snetmcom
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Location: USA

Join Date: Oct 2008
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Quote:
Originally Posted by juan View Post
When converting from colorspace to basespace, if you reach an error (no color, aka "4" or "."), you have 4 possibilities for the rest of the read. How do you determine the correct one?

Example:
Colorspace T000.00
Is basespace TTTTN followed by AA, CC, GG or TT

Which is correct? If you have a sequencing error early in the read, such as position 1 or 2 it goes in the garbage?
You map your reads in colorspace. You do not decode the strand and then map. This gives you the benefits of 2base encoding while detecting errors throughout the tag.
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