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Daniel-Liu-c0deb0t / UMICollapse

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.
MIT License
62 stars 8 forks source link

keep unmapped reads #15

Open karlkashofer opened 2 years ago

karlkashofer commented 2 years ago

Is it somehow possible to keep the unmapped reads in the output file, or at least write out the unmapped reads to a separate file instead of discarding them ?

Daniel-Liu-c0deb0t commented 2 years ago

Not at the moment. You can work around this by filtering out unmapped reads from your file before deduplication with samtools like here.