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muellan / metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
GNU General Public License v3.0
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Out file interpretation #17

Open bielasilva opened 3 years ago

bielasilva commented 3 years ago

Hello, I'm having trouble interpreting the per-read mapping report, specifically the taxid. I noticed there are some negative ones and when plotting with KronaTools most are not identified but some are classified as Eukaryota. Could you please clarify what they are?

Is there a recommended tool for plotting the results?

Thank you.

muellan commented 3 years ago

Hi,

since Metacache can classify down to the sequence level and individual sequences do not have an official NCBI taxid, we use negative taxids to identify the individual sequences in the current database. If you don't want/need that you can restrict the classification output with the option -lowest <rank name>, so e.g., -lowest species or -lowest subspecies.

bielasilva commented 3 years ago

Ah, got it! Thank you, I'll do that!