When using --longReads with the meganizing tool, taxonomical results in MEGAN will correctly be displayed as “number of aligned bases”, while for functional annotations (I tried KEGG) the y-axis will display “number of reads”.
Are you referring to the charts that MEGAN produces? Like this one:
If so, please note that yesterday I uploaded a new release of MEGAN that fixes this problem…
Yes, that’s what I meant. Thanks for the update fixing this!