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Old 09-27-2011, 06:50 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,088
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Kay,

If you are going to use the new version of CASAVA (v.1.8) you may need to remove the reads that would be normally filtered out before you do the alignments. See "dawe's" post on this page: http://seqanswers.com/forums/showthr...highlight=dawe

Illumina is supposed to come out with a update for CASAVA (http://seqanswers.com/forums/showthread.php?t=14316) that will do this automatically in October.
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