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Old 08-21-2010, 03:35 PM   #26
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Location: San Diego, CA

Join Date: May 2010
Posts: 116

Instead of using Z=100 on the whole data set, it might be a better (meaning faster) idea to first align the data set with Z=1 (default value) and then realign the ones that do not satisfy your alignment criteria with a higher value for Z. This should speed up the process if you assume that a high number of the reads will map to the reference.
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