I am working on the results from Humann3. However, I can not find any link file for Metacyc pathway to the EC gene family. For example, I want to know how many EC gene family and which EC gene family involved in the specific metacyc pathway. Could you please help me?
ECs and MetaCyc reactions are mostly a one-to-one mapping. If you quantify reactions directly from your sample and then attach names to them (with the
rename_table scripts, respectively) you can see the ECs assigned to each reaction. We go over this specific example in the HUMAnN 3 tutorial:
Thank you so much for your reply. I only have the results from HUMAnN3 which only contains EC families and Metacyc pathways names, separately in two files. Could you please help me give me a file which may have a list that have EC and Metacyc mapping? Or please tell me that where could I find these kinds of files?
If you install the HUMAnN “utility mapping database” it will include the mapping of MetaCyc reaction codes to names, and the EC numbers are embedded in those names. Please see the
humann_databases script and associated help info.