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CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets
MIT License
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How to collapse reads in bam from the result of UMI-tools group #501

Closed camelest closed 2 years ago

camelest commented 2 years ago

Hi, first of all, thank you for the wonderful tool.

I have a question regarding UMI-tools dedup.

Is there a way to output UMI-collapsed bam files using the results from UMI-tools group, without running UMI-tools dedup again? In other word, how to dedup a bam file when UMI tags are added and read grouping are already done?

Thank you in advance for your help.

Best,

IanSudbery commented 2 years ago

We don't have a way to do this in UMI-tools itself I'm afraid, you would need to write the code yourself.

camelest commented 2 years ago

I see, thank you for your prompt reply. Best,