I was wondering if exporting annotations via [export] [annotations in gff format] is a feature restricted only to the ultimate edition?
I have DIAMOND results (+ accompanying FASTA) file that I imported into MEGAN CE (6.10.6) together with the eggNOG mapping file, using the longReads LCA method. When I select nodes, individual reads in the longread inspector or OG’s the eggnog viewer, the [export] [annotations in gff format] remains greyed out, and is not clickable.
Anything I am doing wrong here on my end, or is what I am trying to simply not supported? Any insight is greatly appreciated!
All the best,
did you meganize your daa files?
You can find daa-meganizer in the tools folder in Megan application.
In this case, the imported file was a pair-wise format (generated with diamond view --outfmt 0). The import itself however works fine, as does the mapping to the eggNOG categories. Its’s just specifically exporting nodes/reads into a GFF format that seems to be not working.
I can check if I can reproduce this issue using the original DAA file if that helps?
I just tested this out, and when I use the meganize functionality, it does seem to work. So it seems exporting to GFF can only be done when the DAA files are used, and not when importing txt(pair-wise) and fasta combinations (as in import from blast)?
GFF export is available in both the Community and Ultimate Editions.
It works also for data imported from pairwise blast files. Not sure what the problem is, please give me access to a file that exhibits the problem and I will take a look.
Thanks for checking this out. I have uploaded subset of my data in a zip with txt, fasta, megan log file and steps to reproduce here: https://drive.google.com/file/d/10h6gF-lg7aPUnBY98q6xVuz4jz3kP9mm/view
If you need anything else let me know,