Hello,
I want to run HUManN3 with a custom databse on the raw files provided in the ibdmdb. From what I gather the raw files here have already been quality controlled and filtered with kneaddata. I’m a little confused because from the log file a single output is given wheras the rawfiles are still R1 and R2. Do I need to run kneaddata + trimmomatic before humann in these samples? If not, do I just cat the R1 and R2 together and run humann? Thank you for your help.