get.oturep to get representative sequences for each OTU


I am trying to use the command get.oturep to get representative sequences for each OTU as follows:

get.oturep(,count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table, method=abundance)

I did not use .dist file here because it would probably need more than 24 hrs to generate the .dist file.

Count table was generated, listing the representative sequence ids and their numbers in every sample. But I do not know which is the corresponding OTU for that representative sequence. Is there anyway I can link OTU to its representative sequence id?

I have a list file that listing OTUs and all the sequence ids, but it is too big to open in excel.

Thanks for your help!


You should just be able to pass in the fasta file that corresponds to stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table and it will pick the representative sequences. Do you get an error when passing in the fasta file?

Thanks dwaite! I figured it out…