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Old 04-07-2009, 12:10 PM   #3
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Location: Sweden

Join Date: Mar 2008
Posts: 324

Definitely unmasked. The repeats masked by repeatmasker (alu, line, sine, mir etc) do contain unque sequences, and probably using masked reference would lead to false alignments of reads from repeats if you allow several mismatches. chr.fa files are also repeatmasked but to lowercase rather than N:s so this information can still be used by some aligners-
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