Need help in importing DAA file

User Questions
1

Hi everyone,
I use the Megan-Dimond pipeline in Galaxy Europe.
I have generated the DAA file with the diamond aligner.
the DAA file is 65 GB in Size.
I am confused about what should I do now with this big file.
Can someone suggest to me how can I analyse my data with this DAA file ?

2

I am not associated with MEGAN, but I have been processing data for a about two months now with MEGAN6 UE and can attempt to help.

  1. That is a very large daa file… is this somehow a bunch of samples combined? Either way, you may want to save this file somewhere else before processing further with MEGAN as the next step (meganizing) adds more information to the current DAA file.

  2. You then want to ‘meganize’ the daa file, which is annotating the DAA file against many taxonomic and functional gene databases. I have not used MEGAN in Galaxy, but on my computing cluster I use the daa-meganizer function (found in the ‘tools’ directory). You will want to specify the mapping database (-mdb), which for me is ‘megan-map-Feb2022-ue.db.’ You can download here or perhaps it is already uploaded somewhere in Galaxy?. I am using the Ultimate Edition, which has KEGG database that is why my MEGAN mapping file has the ‘ue’ in the .db file, not sure what version you are using on Galaxy.

  3. For me, I have multiple samples to compare, and thus have a mapping file with a specific set of treatment factors associated with file names (the entire DAA filename without ‘.daa’ at the end), and use the command compute-comparison for the meganized DAA files.

  4. You will likely want to save the file using daa2info. There are option for the type of file output read-to-count (-r2c) or class-to-count (-c2c), which is followed by the list of databases that you meganized against. I am still figuring out the best way to extract data into .csv files for more statistical analysis in R (posting a question about this now).

Sorry, that was a lot. Hope some of it helps.

Good luck!

3

I can only add that while meganizing does add stuff to the bottom of a DAA file, it does not change anything else, and so meganizing should never corrupt a DAA file, so hopefully, making a copy should not be necessary…