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Old 10-01-2013, 12:37 PM   #4
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Originally Posted by A_Morozov View Post
Can anyone please explain me why the default behaviour is to randomly choose one of mappings? Making sense of multiple mappings is big enough headache without mapper hiding half the results from you.
I guess it's so that coverage across repetitive regions is comparable to that of unique regions. If you give all the reads to each of 10 repetitive regions, coverage at each will be 10x higher than the rest of the genome.

If a region is repeated 100 times, it will have 100x coverage as compared to the rest of the genome, which would really screw with trying to count how well the rest of the genome is covered.
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