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Question: Align.seq metagenomic data
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gravatar for balagenotech
8 months ago by
balagenotech • 10
balagenotech • 10 wrote:

I am new to galaxy and i am using metagenomic data after unqiue.seqs step i use the unique.reads for alignment using align.seq with greengeen 16 S alignment reference database but it showed error Like this Reading in the alignment.template.dat template sequences... [WARNING]: We found more than 25% of the bases in sequence 4484395 to be ambiguous. Mothur is not setup to process protein sequences.
alignment align.seq mothur galaxy input • 272 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by balagenotech • 10
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gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

As the error states, a protein fasta dataset cannot be used as input. Nucleotide fasta is required.

I retested the tool using the sample data in this tutorial (nucleotide) and it worked fine, so I don't think there is a tool problem. http://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html

If your input is in nucleotide format, and the job still errors this way, please send in a bug report if working at https://usegalaxy.org or can reproduce the problem there. If there is a new bug or suspected bug, we will want to look at it. After review, we will reply with usage advice or get the bug fixed. Please include a link to this question in the comments of the bug report so we can link the two. https://galaxyproject.org/issues/

Galaxy tutorials: https://galaxyproject.org/learn/

Galaxy support FAQs: https://galaxyproject.org/support/

Hope that helps! Jen, Galaxy team
ADD COMMENT • link written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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