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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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Secondary alignments #54

Closed Soniazumalave closed 5 years ago

Soniazumalave commented 6 years ago

Hi,

I would like to know if there is any parameter to allow the generation of secondary alignments. Thank you in advance.

Sonia

darth-donut commented 5 years ago

Hi,

Same question here, is it possible to output secondary alignments?

There's a tandem repeat region in one of the chromosome of a transgenic genome and NGMLR seems to only map the first repeat, leaving the others blank.

Cheers, Harry

fritzsedlazeck commented 5 years ago

Hi, sorry NGMLR supports secondary alignments, but only as split reads. Ie. if two parts of a read map to different region. however, not if one part of a read is mapped to two different regions. I hope that clears it up. Cheers Fritz