Output of cluster vs cluster.split

I was going through the MiSeq SOP and was curious what the output files’ extensions of cluster versus cluster.split are (specifically under the “Preparing for Analysis” section, “OTUs” subsection)? I ran cluster rather than the cluster.split command and one of the output files was this:


When I went to run the make.shared command, I noticed on the SOP, the list file used has a slightly different extension than my list file:

SOP: …pick.pick.pick.opti_mcc.unique_list.list


My list file: …pick.pick.pick.opti_mcc.list

Is the list file used for make.shared (in the SOP) generated from the cluster.split command? So I assume from that point forward, I may have slightly different file extensions because I ran cluster command, but nothing else will have changed? Or did I make a mistake somewhere?


The “unique_list” tag is added when you cluster with a count file. This tag reminds you that the list file only contains the unique sequences. When you cluster using a names file then this tag is omitted because the duplicate names are included in the list file.