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andersen-lab / Freyja

Depth-weighted De-Mixing
BSD 2-Clause "Simplified" License
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Abundance 100% #177

Closed Linnet111 closed 11 months ago

Linnet111 commented 11 months ago

Hi Josh,

Just had a quick question- does the abundance of the lineages have to add up to 100% in total for a particular sample? Is the algorithm created that way or are variations in the total abundance expected?

Thank You

Kind regards Linnet Immaraj

joshuailevy commented 11 months ago

Hi Linnet,

When running Freyja using the default parameters, lineage frequencies less than the threshold (0.1%) will not be included in the output, so as to not report tons of low level false positives. As a result, the sum may not always add up to 100%. You can adjust this parameter using the --eps command though. Setting it to something small should lead to the sum equalling 100%.

Best, Josh

Linnet111 commented 11 months ago

Thank You! Appreciated!

joshuailevy commented 11 months ago

No problem! :)