I’ve being using Humann2 for taxanomic and functional profiling of metagenomic samples along with total RNA seq analysis and I’ve been seeing some confusing results. Aligning RNA reads to the Refseq database I identified a significant proportion or reads which aligned to mycobacterium species, looking at the humann2 pathway abundance I can see the mycobacterium peptidoglycan synthesis pathway was also id’d in most of the samples.
However, metaphlan2 was unable to ID mycobacterium in any of the samples. I’m thinking that the abundance may be very low, given that can I run metaphlan2 with a minimum abundance filter set to 0 so I see absolutely everything ID’d within the sample, even if it’s only a few reads? If not, can anyone suggest why I can find mycobacterial reads from RNA data and humann2 analysis but not metaphlan?