The bioBakery help forum

Metatranscriptomics tool

I hope you are doing well amid this pandemic. I was recently introduced to your galaxy website to use the tools there—which has been really fantastic. I used the maaslin2 to analyze my metagenomics data but it only gives results in notch box plots. I have both my metagenomics data and metatranscriptomics data in table form (excel and others). What I am having a challenge with is finding a tool that can merge these two datasets so I can link the microbes to the function. I wanted to ask which of the tools from your lab’s website (not the galaxy one-but the Harvard one) would work best to do that?

Thank you in advance for your help.

HUMAnN can analyze both metagenomes and metatranscriptomes. We offer some suggestions for doing that here:

Since your samples are paired, you can look for changes in expression (RNA abundance) while controlling for gene copy number (DNA abundance). You can do this either by computing RNA/DNA ratios and modeling against those (or) by including a gene’s DNA abundance as a covariate in a model of the gene’s expression. (I say “gene” in the examples above, but the same logic applies to any function you’re interested in.)