Thread: 32bp?
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Old 11-08-2008, 09:39 AM   #3
dcjamison
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Location: Cincinnati

Join Date: Oct 2008
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The first 32 bases are used for the seed alignment, then the alignment is extended for the bases beyond 32.

For GA Pipeline 0.3 and newer, there is a Gerald analysis mode called eland_extended which takes the top potential alignments and extends all of them, scores the alignments with a phred-like score, then reports back the best scoring alignment. So, while only the first 32 bases are used for the seed alignment, all bases are used to determine the best match.
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