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Old 07-15-2009, 09:51 AM   #2
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
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Originally Posted by pfranchini View Post
In which way I can filter the information of unique and repeat hits of the reads to the reference with Maq? There is a way to obtain a global statistic of the mapping? Thanx

You can use the mapping quality. Zero mapping quality means there were multiple equally likely mappings, and greater than zero means there was a most likely mapping found. If you want some general mapping statistics, you could convert your .map file to the SAM/BAM format and use the samtools "flagstat" command.
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