Question: Problem with Align.Seqs
0
gravatar for cjroy
5 months ago by
cjroy0
cjroy0 wrote:

Hello I am trying to run my fasta output file from Unique.Seqs with Align.Seqs and I am trying to assign my Silva reference but all it says is no options available and the only reference template I can select is Cashed reference or your history. What might I be doing wrong? Thank you

ADD COMMENTlink modified 5 months ago • written 5 months ago by cjroy0

ok me again so I figured out that I need to upload my own silva fasta file. I cannot find this silva.v4.fasta file that this protocol 16S Microbial Analysis with Mothur is asking for. I uploaded the most recent release from the silva website but that does not seem to be working...unless i messed up somewhere in the earlier steps. if someone knows the secret can you please let me in on it? I am a new user if you didn't pick up on that already...just trying to find my way. Thank you!!

ADD REPLYlink written 5 months ago by cjroy0
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

How to retrieve the tutorial data for https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html is explained in the section titled Importing the data into Galaxy.

Specifically, the reference.data.zip archive contains the fasta data used in the tutorial: https://zenodo.org/record/165147/files/reference_data.zip

FAQ: https://galaxyproject.org/support/loading-data/

Hope that helps! Jen, Galaxy team

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k
0
gravatar for cjroy
5 months ago by
cjroy0
cjroy0 wrote:

Oh nuts Jen,

I totally missed that. I am working on my own data with this SOP and skimmed right past that because my sample data was already imported. Sorry to bother you for something so easy to fix. Thank you for your help and immediate response!! much appreciated

Julie

ADD COMMENTlink written 5 months ago by cjroy0
0
gravatar for cjroy
5 months ago by
cjroy0
cjroy0 wrote:

can you also analyze 18s MiSeq runs with this protocol?

ADD COMMENTlink written 5 months ago by cjroy0

In general, yes, but with some changes. You might also want to contact the lab that authored the tools/protocol for best practice advice. Please see the source SOP/author contacts linked from the tutorial for details.

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
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