I am interested in working with the Humann2 output from the metagenomics (MGX) and metatranscriptomics (MTX) IBDMDB data - specifically the gene families quantification.
To download a large number of these outputs, I’m using the FTP server (ftp.broadinstitute.org).
However, I’m confused about where to look for samples. Within the
MGX subdirectory, one finds
Each of these contains humann2 output files. There is a great deal of overlap between the sample names, although the contents of the files are not the same. What is the difference between these directories?