Hi,
i am new to Mothur, so i dont have enough knowledge about it. I want to analyze biom file (biom format) which i took from QIIME.
Is Mothur accepts QIIME biom file ? If it does, then how can i import in Mothur for Alpha and Beta diversity.
Best !
Shashank
You can use make.shared to generate a shared file from a biom file
http://www.mothur.org/wiki/Make.shared
Thank you for the information.
when i used the command in Mothur, i got an error
[b]mothur > make.shared(biom=F16_closed_ref.biom)
Output File Names:
F16_closed_ref.shared
mothur >
[ERROR]: You are missing (
Invalid.[/b]
and when i saw the file, its empty. How can i resolve this issue ?
Best!
shashank
The error message is because you added an extra line ending when you copied and pasted or when you were typing. It’s not meaningful. You’re saying that F16_closed_ref.shared is empty? What version number of mothur and operating system are you using?
Pat
i tried again by writing the above command, now i won’t get any error, though the output file i obtained is F16_closed_ref.shared, which is empty.
the version i am using is
mothur v.1.25.0
Distributor ID: Ubuntu
Description: Ubuntu 12.04.5 LTS
Release: 12.04
Codename: precise
You should upgrade your version of mothur, http://www.mothur.org/wiki/Download_mothur.