16% unmapped, 78% unintegrated reads for pathway analysis in human gut metagenome

Hi all,

I have 50 human gut metagenomics data. After running humann3, I got 16%±2% unmapped reads and 78%±2% unintegrated reads in the pathway abundance output file. Regarding the proportion, I have 2 questions. Hope to have your comments and suggestions.

  1. Seems that the proportion of unmapped reads is reasonable. How about the proportion of unintegrated reads? Is it too high?

  2. If the proportion of unintegrated reads is also reasonable, it means that majority of the reads cannot be aligned to a metabolic pathways. Then does it make sense to work on such a small proportion of aligned pathways?

Best regards,

Hi @lauren.j.mciver,

Any idea on the high proportion of unintegrated reads for the pathway analysis?