The make.shared command created a rabund file for each group, but since revision 1.36.0 these rabund files are not outputted and the get.rabund command has to be used instead, Now, the get.rabund command takes a list parameer but not a group parameter. How can I create rabund files for each of the samples? I’m trying to run the Sogin data analysis but a lot of things have changed in Mothur since this was written. Thanks,
The get.rabund command allows you to enter a count file. If you do not have a count file you can create one with the names and group file associated with your list file. Be sure your count file includes group information or you will just get an rabund for the entire dataset.
mothur > get.rabund(list=yourListFile, count=yourCountFile)
Can you move up to the MiSeq SOP? As you note the Sogin analysis page is really out of date and is only left up for historical purposes. I’m not actually sure what one would need the rabund files for since things like summary.single, rarefaction.single, etc will all take a shared file.
We will add the shared file type to the get.rabund command for our next release. Thanks for the suggestion!