I am hoping someone could help me troubleshoot an issue which involves very low mapping rates (~10-15%) for our whole genome sequencing data using Kraken 2. Samples are gut microbiome samples from patients with heart disease, sequenced on Illumina HiSeq X, paired end 150bp, 350 bp insert. The aforementioned mapping rate is after we use Kneaddata to remove human reads, adapters, etc.
1) This is my first time using metagenomics for gut microbiome, but, as best as I can tell based on the literature and speaking to some folks who have worked with gut microbiome metagenomics and Kraken 2, the "expected" mapping rate for human gut microbiome is >50% -- is this indeed correct? When we use Humann2 for functional assessment for the same samples, there is a 50-60% mapping rate.
2) What may be the reason that I am getting such low mapping rate?
Thanks so much for your help, LT