Hi, I've been using lastz to map some 454 reads to a reference sequence on galaxy. I'm not clear on what the mapping modes do for the analysis. If I am already setting a cut-off value for the percent identity for reporting matches then what exactly does the mode setting do? In the tutorial you set a roche-454 98% mode based for a re-sequencing example and then set the identity to 90%, what parameters in lastz does the mapping mode change?
thanks, H
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