I am trying to assign reads to functional categories using SEED and EggNog and used the approach described here, but with the ncbi env_nr instead of the nr database:
290 hits are found, but they are classified as “not assigned” in MEGAN, so I guess I am doing something wrong.
The commands I use:
Hello! Where did you find env_nr.gz? If you download the env_nr database from the BLAST website, it gives you 3 separate env_nr.tar.gz files with a bunch of different format files inside. Diamond needs a single .fa file to makedb, but env_nr doesn’t come like that. Any idea how to use env_nr with diamond? I tried some stuff from here https://www.uppmax.uu.se/resources/databases/diamond-protein-alignment-databases/ but it doesn’t work. Thanks!