previously on Megan6, im able to get subspecies-level viruses to show up. (e.g. Dengue virus 1, dengue virus 2, etc)
but on Megan7 currently is will only show up to species (e.g. Orthoflavivirus denguei) using the same blast result.
unsure if this is a bug, or just a feature not implemented yet.
Hi @OmarKR,
I’m not sure if I understood correctly. Have you re-MEGANIZED your file? MEGAN6 files are not compatible with MEGAN7 (assuming you’re using the DAA format). If you’ve used new mappings, there might be some accessions that now have mappings which previously didn’t, causing the LCA to place them at an upper node. When I uncollapse the whole tree, I can see the mentioned taxa.
Regards,
Anupam
hi,
i think yes it’s re-meganized. as in I reimported the blast xml from start, rather than use a megan6 rma as input.
i was wondering if theres a setting i need to toggle, but you say you can go beyond species-level on megan7 by uncollapsing the tree? that’s how i did it in megan6, but for these taxa it did not work. you may be right in that mappings changed, but perhaps in my case the change was not for the better.
which taxa were you talking about in your statement earlier?
im specifically looking at dengue sub-species
What I meant to say is that if I uncollapse the entire tree (default tree, without importing any data), I can see the taxa present, indicating that the taxa is there.
Additionally, as I said re-meganization might have updated MEGAN result, but you cannot uncollapse the tree beyond the level where the LCA places them.
You might want to experiment with the PTC parameter, which could provide results closer to what you’re looking for.
Best regards,
Anupam