I’m running humann3 on paired metagenomes and metatranscriptomes.
I noticed that I have metatranscriptome reads mapping to species that don’t show up in the community profile output.
e.g. there are metatranscriptome reads mapped to Bacteroides fragilis CAG 47, but Bacteroides fragilis CAG 47 does not show up in the corresponding community profile.
When looking at the metaphlan output it seems that Bacteroides fragilis CAG 47 has been grouped together with Bacteroides fragilis. But this is not the case for the gene families output from both the metagenomes and the metatranscriptomes, where these two strains are separate.
And I see the same for multiple species/strains.
Consequently, I cannot reconcile these species/strains transcription information with their relative abundance.
I use the following commands to process the raw reads:
humann3 -i mg.reads.fastq --protein-database path/to/uniref/ --metaphlan /path/to/metaphlan/3.0.1 -o mg.file --threads 4
humann3 -i mt.reads.fastq --protein-database path/to/uniref/ --metaphlan /path/to/metaphlan/3.0.1 --taxonomic-profile path/to/corresponding_metaphlan_bugs_list.tsv -o mt.file --threads 4
Am I misunderstanding how to process paired metagenomes and metatranscriptomes with humann3?
Thank you for your help!