The bioBakery help forum

Analyzing GO categories in HUMANn2

I am interested in analyzing differential abundance of GO categories from HUMANn2 output. I used the “humann2_regroup_table” command to generate GO category summary RPKs from original gene data. However, the output file lists a GO number without a GO category name. For example, it has “GO:0000179” but not a name associated with that GO term. Is there a straightforward way to get the associated GO term, given this output?
combined_gene_names_normalized_GO_2020.7.15.sample.txt (9.7 KB)

You can use the humann_rename_table script to attach human-readable names to any IDs that HUMAnN outputs, including GO terms. (The reason we don’t do this automatically is that it’s often convenient to just attach the names once after merging your samples; if you have the names attached to every sample then it increases the size of the files by ~2x).