Hello all, I wanted to ask the community if I was potentially missing something in my methodology. Essentially, I have a group of MAGs composing of a relatively small family of bacteria. One of these MAGs is my main interest. I've mapped the family of MAGs to a bunch of metagenomics sampling I've found where this one particular MAG dwells. Now some of these samples have metatranscriptomic data and I would like to map my MAGs of interest to the metatranscriptomic data to see gene expression across all of these different sampling sites (as well as across time as some are longitudinal). I am wondering if there are any biases, or potential errors of mapping my MAGs of interest by themselves to samples? My current method is to map the CDS.fna file to these samples, but I am curious is there is something I am inherently missing. Any input would be appreciated!
