Get.oturep files

Commands in mothur
1

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

2

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?

3

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)
4

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