Magan, after run via command line, can I use the interface to view and look around results?

Question

[cara78]

Hello again,

Another MEGAN question please. I am preparing as much as possible because my file is so big. Running on server and want to min mistakes as much as possible, don't want to waste days work.

I am running on the command line. I will submit my files of blast and fasta in command file.

Once the files have been processed via the command line is it possible to then take the output file(S) and see them with the use of the interface. So can have look around.

or should I said what results I want in the command file, all at once.

Thanks

Answer 1

[lelle]

The output *.rma files can be opened with the graphical user interface.

Maybe you could do a test run with a sub-sample of your sequences (lets say the first 1000) to test this kind of things?

Answer 2

[dapregi]

MEGAN will create an RMA file (MEGAN specific format), which contains the results of the taxonomic assignment. Typically, after generating a RMA file, you can then open it with the program and interact with the results. You can even interact with the output through the command line as well.

Take into account that the RMA file content depends on the LCA parameters. So if you want to change that parameters, MEGAN will initiate the recalculation of all the taxonomic classification.

Besides, I recommend you to subset your data and run some tests to familiarize with the software.