Bowtie clearly indicates in its manual that it will randomly assign any read for which there are multiple equally valid alignments. I can not see any such discussion regarding the "mem" aligner for BWA. Can anyone tell me how BWA handles multiple alignments per read, and what the default settings are?
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Originally posted by A_Morozov View PostCan 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.
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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