I also don’t understand why some reads are not assigned. One example can be broken down to one hit like
query1 gi|998520486|ref|XP_015521226.1|tax|441921| 100.000 8 0 0 1 8 92 99 57 31.2
I expected that the read was assigned to Neodiprion lecontei, as the taxid is correctly interpreted my MEGAN. However, the read is not assigned. Min Score is set to 1, Max Expected to 1000, Min Support Percent to 0 (off), Min Support to 1. (Actually, the read has many more hits.) Am I missing something? Thanks for any suggestions.
Daniel replied to my question:
The taxon is present in the taxonomy. What is minSupport and minSupportPercent set to? Try setting minSupport=1 and minSupportPercent=0
Setting minSupportPercent to 0 worked for me: The Min Support Percent item is used to set a threshold for the minimum support that a taxon requires, as a percentage of assigned reads. This feature is turned off by setting the value to 0.
Thanks, minSupport and minSupportPercent were set as you suggested (see my message). Might be that it’s something obvious that I’m doing wrong, but I just can’t find the reason. If you like, you can try to load the one hit (a one-line blast file) from my message into MEGAN.
I tried your hit - and it gives me the same result as you - into Not assigned - not sure why (I’m new to MEGAN)