Hello,
Does anyone has a Mothur-friendly file of the MiDAS database, or does anyone knows where I could get one?
Regards,
Elliston Vallarino
Hi Elliston - I forget whether you have access to a mac/linux environment, but if you do, you can do the following after downloading files from these two links…
https://www.midasfieldguide.org/files/downloads/taxonomies/QIIME%20txt%20file%20MiDAS%204.8.1.txt
https://www.midasfieldguide.org/files/downloads/taxonomies/QIIME%20Fasta%20file%20MiDAS%204.8.1.fa
cat QIIME\ txt\ file\ MiDAS\ 4.8.1.txt | sed -e "s/ //g" | sed -e "s/$/;/" > midas.taxonomy
mv QIIME\ Fasta\ file\ MiDAS\ 4.8.1.fa midas.fasta
I put a compressed directory with both files on my google drive. Let me know if you can’t access it or if it’s doing weird things when you try to use it.
Pat
Pat
Hello,
Thank you very much for the files. I was able to download them from the google drive. I could also download them from the links and use your command line instructions.
Now, I am trying to use them in Mothur, but I have this message:
mothur > align.seqs(fasta = ecoli.v3.fasta, reference = midas.fasta)
Using 12 processors.
Reading in the midas.fasta template sequences... [ERROR]: template is not aligned, aborting.
DONE.
It took 0 to read 0 sequences.
How do I fix this problem? How do I get the Midas file aligned? Could I maybe align it to the Silva file I used for mothur?
Right- you’ll have to align midas.fasta to the silva reference file. But for classification the sequences don’t need to align the reference.
Pat
Hello,
Yes, this worked, and I was able to do the analysis. Thank you very much!
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