Hi,
I am wondering if anyone here might understand what is going on with exporting feature tables with their phylogenetic trees because I cannot get it to work. I tried to use the ncbi.tre file, and I think the sample tree (file > export > tree) should work as well, but I cannot get them to import into QIIME2. I posted this issue on the QIIME2 forum as well: https://forum.qiime2.org/t/importing-phylogenetic-tree-from-megan/21160/4.
Has anyone else tried to do something similar?
Hello,
I wanted to update this post because I am still having issues. If you see the qiime2 support, there was no simple fix.
The issue is that when I select > all leaves or select > rank > species of a tree and export as a biom file, the IDs do not match the leaves of the ncbi.tre file provided with MEGAN. Is there something I am doing wrong in MEGAN? Is there a way to avoid any classifications that are internal nodes in the ncbi.tre file? Any advice on this issue would be appreciated.
Hi,
I had the same issue when I try to export the BIOM files and tree and import them to R as phyloseq object. Maybe before you export the tree, select the options “show ID” in 'Tree" tab. Meaning nowit will export tree with IDs instead of names of taxa. This helps me to match tip$lables in tree file and the tax_table of BIOM files after converting to phyloseq object.
I hope this help.
Lenny