mothur

Get.oturep files

hello,

I have a question regarding the get.oturep command. My goal is to generate a file that contains a sequence for each OTU, so that I may search (blast) the data set for a specific 16s sequence.

I have read through the tutorial, but I am confused about which files to use for this command. In the example provided on the wiki sop page (below), I am wondering which .list file and .fasta file do we use? I have generated one .list file by running through the standard pipeline, is this what I should use? When I viewed the amazon.fasta file in the tutorial, it showed each otu and its sequence; how do I generate that?

get.oturep(phylip=98_sq_phylip_amazon.dist, list=98_sq_phylip_amazon.an.list, fasta=amazon.fasta)

Regards,

Micah

After reading through more questions posted by others on the forum, I think that maybe I actually want to run bin.seqs (this way I can view all the sequences, not just the representative sequences, correct?) If this is true, I suppose my same questions still apply–what are the appropriate .list and .fasta files to use for this?

You likely want get.oturep. If you’re following the MiSeq SOP, then you likely want to use something like this…

mothur > get.oturep(list=98_sq_phylip_amazon.an.unique_list, count=amazon.count_table, method=abundance)

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