The get.rabund command will generate an rabund file based on the OTU data that you have read into mothur.
mothur > get.rabund(list=amazon.fn.list)
mothur > get.rabund(sabund=amazon.fn.sabund)
mothur > get.rabund(shared=amazon.an.shared)
If the list file contains multiple lines and you are only interested in a subset of those lines you can use the label option:
mothur > get.rabund(list=amazon.fn.list, label=unique-0.03-0.10-0.20)
By default the data in the rabund file are not sorted. That is they are in the same order as the OTUs in your list file. If you would like these data to be sorted by their abundance you need to use the sorted option:
mothur > get.rabund(list=amazon.fn.list, sorted=T)
You can use the groups parameter to specify which groups you want included in your analysis.
mothur > get.rabund(shared=amazon.shared, groups=pasture)
If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file with the get.rabund command.
mothur > get.rabund(list=amazon.an.unique_list, count=amazon.count_table)
- 1.31.0 - Added count parameter.
- 1.41.0 - Adds shared and groups options. #325