Specify taxonomic level about centrifuge HOT 5 CLOSED

+1

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I have the same question.

Is "+1" an answer

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+1

from centrifuge.

+1

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Centrifuge assigns the reads to the lowest possible taxonomy level. I just uploaded a script "centrifuge-promote" that promote the taxonomy level to user-specified level.

centrifuge-promote takes three parameters in the order of: prefix of the index, centrifuge output file, taxonomy level. For example, you can run it like:
./centrifuge-promote p_compressed centrifuge_output.txt family > centrifuge_output_family.txt

There may be some assignments associated with taxonomy who can't trace to the specified taxonomy level or already higher than that level. In that case, I does not change their output information.

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