Hi,
I have a question about the assignment of reads to taxa. If I inspect the reads, I see that there are some question marks for reads with the highest score. How can I properly assign all of these? I’ve been using the megan-nucl-Jan201.db mapping file (I believe that’s the most recent?).
This also results in a lot of unassigned reads, while the reads still meet the given parameters (e.g. 90% identity), but it seems that the references just don’t get classified.
Thank you!
Meriam
This is might be due to the fact that the current mapping database is from Jan 2021 and you may be using a newer version of NCBI-nr. I will create a new mapping database bu the end of this month.
Hey! Without trying to rush anyone, may I ask when the new mapping file will be published online? 
Hello, Daniel!
Do you have some idea when you will release the new mapping database? I’m asking it because when I ran my shotgun samples against a new version of NCBI-nr (november 2021) using DIAMOND and after meganized them, I realized that all eukaryota assignments in taxonomic tree were generic while the Bacteria assignments were more specific. For example, I had 32,969 assignments to Opisthokonta (in the tree) and no subclades; however, when you check this clade in the “Inspect” tool, there are several specific assignments for different species (e.g Alternaria alternata and others). Researching in the forum, I guess that a new database could solve this specific question. There is another topic in the forum that is related to this - MEGAN sorting all alignments as unclassified -
Regards,
Fabyano Lopes
