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CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets
MIT License
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--multimapping-detection-method Options documentation #556

Closed gavin-peng closed 1 year ago

gavin-peng commented 2 years ago

Hi, the documentation states the options are NH/X0/XT, but could you explain which tag represents which option? I know the options are lowest number of mapping coordinates and highest mapping quality, but which one is which?

IanSudbery commented 2 years ago

NH, X0 and XT are all different ways of identifying the number of locations to which a read maps, used by different mappers. If you use any of these three tags, reads will be prioritised on the number of locations a read maps to (lower is better). If you do not set this option, then mapping quality is used.