I am working with reads from oxford nanopore sequencing data. They are longer reads but lower quality.
After running a diamond blastx with long read setting, I want to use MEGAN’s LCA algorithm to assign each read a taxa and a function then explore this data in KEGG.
I have tried working with .daa and .m8 files.
I have played around with reducing the LCA params but I’m not sure what they all mean.
Even when I input what I think are more lenient params, every read is put into the Not Assigned group.
This is odd since the blastx has assigned a taxa and a protein name to the reads.