I’m trying to build my own mapping file to eggNOG categories, as the file I need to analyze is a CSV file containing read counts assigned to IDs other than RefSeq IDs. If I got it right, the mapping file I need to provide must be a synonyms file in which the first column should be the IDs used in the CSV file I want to analyze, and the second column should be the COGs and NOGs categories corresponding to each of these IDs - is that correct?
I tried to provide a synonyms mapping file such as this, but the program wasn’t able to load any lines of this file, the message dialog says “invalid id” to every COG and NOG I used in the second column of my synonyms file. Weird thing is that the COGs and NOGs I used in my tentative synonyms mapping file are exactly the same as those appearing in the eggNOG window, but I get no assignments anyway.
What am I misconceiving here? What is the valid ID format for COGs and NOGs to make my mapping file readable by MEGAN? It would also be of much help if someone could provide the mapping file to eggNOG IDs in a format other than the binary file, so I can try to understand how it is interpreted by MEGAN and adjust my own mapping file in the same format.