Question: multimapping handling

brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

https://arxiv.org/abs/1401.1129

MIT License

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Closed weedcentipede closed 4 years ago

weedcentipede commented 4 years ago

Hello there, Quick question, how does bwa-meth handles reads multimapped?, for examples, reads mapping to transposable elements.

Cheers, Luis Alfonso.

brentp commented 4 years ago

multi-mapped reads will have a lower mapping quality from bwa-mem, often zero. bwa-meth doesn't do anything beyond that

weedcentipede commented 4 years ago

Thanks for the quick answer!, I'll have it into account when I'm extracting the methylations

weedcentipede commented 4 years ago

Sorry, to bother again, I would like to know if multimapped reads are reported by choosing one location randomly or for all locations they map

brentp commented 4 years ago

this is handled by bwa-mem. you can look there for the details. my understanding is that it will report the first $n with a mapping quality of 0.