Why am I getting a species assigned for reads with more than 1 match to different species?


#1

Hello.

I ran “blastn” against a custom reference of 16 genomes and loaded the output into MEGAN with the following parameters (that can also be seen at the bottom of the screenshot):

MinScore: 35
TopPercent: 10
MinSupportPercent: 0.005
MinSupport: 1
LCA algo: weighted
Percent to Cover: 80

As seen below, a read that was assigned to Linum also has matches aligning to Castanea, one of each even with a higher score than the top scored for Linum.

How can I improve the specificity of the LCA algo for these situations?

Thanks in advance,
Daniel