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Need a precision on Dragmap's alignment behavior in duplicated regions #60

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lucmarchandhsj opened this issue Dec 18, 2023 · 0 comments
Open

Need a precision on Dragmap's alignment behavior in duplicated regions #60

lucmarchandhsj opened this issue Dec 18, 2023 · 0 comments

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@lucmarchandhsj
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As far as I know, typical bwa behavior in case a read matches perfectly at multiple locations on the genome is that it randomly picks a primary alignment location and put the others as secondary alignment. How does Dragmap do it? I have reads that could fit a gene and it's pseudogene but they seem to all land on the pseudogene for some reasons. Is there a switch to change that behavior?
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