Dear colleagues,
I am working on shotgun metagenomics with hamster samples and facing a challenge similar to what Rachael described. I have a substantial number of unclassified reads and a significant proportion classified only at the kingdom level (Bacteria).
I am exploring two scenarios: parameter optimization and the impact of the Metaphlan version used.
Any hints or insights to help resolve this issue would be greatly appreciated.
Thank you!
Vinícius.