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metagenome-atlas / Tutorial

A tutorial for Metagenome-Atlas
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Where to find contaminant_references ? #11

Open SilasK opened 1 year ago

SilasK commented 1 year ago

Question from @psychesha21

I’m following the online tutorial in the afternoon and I’ve all the way till the Contminate sequences part, and I don’t know where to find these two sequences:

contaminant_references:
  PhiX: /path/to/databases/phiX174_virus.fa
  host: /path/to/databases/host_genome.fasta
SilasK commented 1 year ago

Answer: The PhiX reference will be automatically downloaded. The host_genome.fasta Should be in the default directory if you ran the setup_codespaces.sh

The ide is to move the host_genome.fasta into the empty databases folder. And Specify the same path for both references.

Alternatively you could specify the relative or absolute path to the host_genome.fasta

Last but not least if you don't add anything to the config.yaml you can also continue the tutorial.