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soedinglab / metaeuk

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
GNU General Public License v3.0
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How can i annotate my eukaryotic MAGs by metaeuk? #92

Open YoungerRen opened 3 weeks ago

YoungerRen commented 3 weeks ago

Dear Elileka: After I extracted the eukaryotic sequences with metarep, I binned the eukaryotic sequences with metawrap, and the resulting MAGs were evaluated for completeness with busco, in which the metaeuk mode was invoked, and the output file contained the metaeuk_output file. Then I want to annotate the MAGs for species, using metaeuk taxtocontig, but I don't quite understand which input files should be? Can you help me with this?

following was the reference code: metaeuk taxtocontig --majority 0.5 --tax-lineage 1 --lca-mode 2 these were my metaeuk_output: image

So do u explain the input file ? or what files do i prepare for metaeuk taxtocontig?

best Yonger

YoungerRen commented 3 weeks ago

My main question is that :what's this data , it's not mentioned in your readme file, only seqTaxDb, are these two the same file?

elileka commented 3 weeks ago

Yes, I am sorry if that was confusing, these two are the same :)

elileka commented 3 weeks ago

The files you need are listed here. The following files you should obtain through your BUSCO run. I haven't run BUSCO myself so I am not sure where they are found inside the directories BUSCO produces...

This file is indeed the seqTaxDb, which can be dowloaded using the databases command, for example:

This is the prefix for the output that will be generated by the call: