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AnantharamanLab / VIBRANT

Virus Identification By iteRative ANnoTation
GNU General Public License v3.0
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How to get AMGs nucleotide sequence? #57

Open fanlu-f opened 2 years ago

fanlu-f commented 2 years ago

I want to map reads to AMGs sequences to get AMGs abundance information. But I do not know how to get AMGs sequences file. I try to use identified protein ID to separate it from prodigal.ffn file. But some protein ID have "fragment" . Would you have some ways to solve this questions.

KrisKieft commented 2 years ago

Rather than pulling from the prodigal.ffn file you can pull from the phages_combined.ffn file. The names should match up with "fragment" prophages and whole phages.