Hi,
I am trying to run the rarefaction.single command on Mothur version 1.21 on Windows 7. My data is stored as an excel worksheet. I have tried to open this excel worksheet on Mothur using the examples given on the rarefaction single wiki page. However, I always get an error stating that “Unable to find name. No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command”.
How do I open my data (on the Excel worksheet) in Mothur?
Apologize for my lack of programming knowledge :S
Thank you.
Sorry you’re having problems. It likely has nothing to do with programming. I suspect you’ve saved your data as an excel spreadsheet instead of as a tab delineated text file. Give that a shot and see how it goes…
Pat
Thank you Dr Schloss. When I saved it as a text file I did not get any results. So, I made a new text file and typed in all my data. Can you please tell me if this is the correct format of data that can be used on mothur? If not what is the correct format?
1 2
2 4
3 1
4 7
5 2
6 1
First column = labels
Second column = number of OTUs
Each label and number of OTU is separated by one tab.
Again, I apologize for my lack of knowledge and thank you for taking the time to help me.
Hi,
This is not a format that mothur will understand. Please see http://www.mothur.org/wiki/List_file to see what a list file should look like.
Pat