How to run rarefaction.single after running cluster.split?


Due to the cluster command only clustering my sequences as “unique” I decided to run the cluster.split command which clustered my sequences at various distances, however, resulted in multiple .list files. I then attempted to merge these .list files together to run rarefaction.single, but the merged file only gives me the results for 100 sequences and then stopped. Is there another way to combine these files so I can run rarefaction analysis?

Thank you!


Hi Tamar,

Have you seen the commands in the MiSeq SOP? A couple of weeks ago I completed the OTU-based analysis there. You’ll see how we use cluster.split, make.shared, rarefaction.single, etc.