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wiki for the mothur software package
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Question on: SILVA v138.1 reference files for arb database; mothur program #104

Closed zhinew15 closed 6 months ago

zhinew15 commented 1 year ago

I want to extract the SILVA reference data from arb in the format of fasta_mothur.eft, which is a customized format. The mothur tutorial told me to create a .eft file, but I can't edit any linux system file through a vnc offered by my university. Is there other mothur compatible format for the SILVA reference?

pschloss commented 1 year ago

Not that I know of. I'd suggest trying to run arb on your local computer to extract the file. Also, just to be clear, except in rare circumstances, you really shouldn't have to go through the process of extracting stuff from the silva files. The fasta and taxonomy files are made accessible on the mothur wiki at https://mothur.org/wiki/silva_reference_files/

On Wed, May 10, 2023 at 10:15 PM zhinew15 @.***> wrote:

I want to extract the SILVA reference data from arb in the format of fasta_mothur.eft, which is a customized format. The mothur tutorial told me to create a .eft file, but I can't edit any linux system file through a vnc offered by my university. Is there other mothur compatible format for the SILVA reference?

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