Reading Uparse Output In Mothur

Question

[vijay]

Dear All,

Can someone suggest me on how to generate a rarefaction curve in mothur using the cluster output from Uparse.?

Cheers,

Vijay

[Josh Herr]

Given than UPARSE is hot off the blocks (it only was released less than 2 weeks ago) I haven't had a chance to give it a run, let alone give it a run in MOTHUR. The output is the same as USEARCH/UCLUST so I don't see how you would generate a rarefaction curve any differently than you would have using the previous versions of the program in MOTHUR.

So, two questions: Were you able to generate rarefaction curves before in MOTHUR using UCLUST/USEARCH? ...and, what have you tried to generate rarefaction curves using UPARSE and what errors are you getting?

[vijay]

Hi Josh,

I was able to generate rarefaction curves using the standard protocols suggested by mothur. I understand that mothur requires a .list or a .rabund file to create a rarefaction file. I had a try at UParse and I got an OTU table from it. I was just curious to know how do I convert this cluster file from Uparse to a .rabund file or a .list file so that it is recognised by mothur.