Hi! I am working with a big data set with over 500 samples, and I used the Mothur MiSeq SOP. I am looking to find representative OTU sequences for only around 20 OTUs. Running get.oturep() using my final.dist file will require a LOT of RAM and will take forever and a half.
Is there a way to get representative OTU sequences for only a select few OTUs?
For context, I am focusing on correlations between bacteria involving one genus of interest.
Hi there - you might try using the method=abundance argument. This will pick the most abundant sequence in the OTU as the representative sequence. We find that this often gives decent results and is far less memory intensive than the distance-based approach.
Pat
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