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.
You can use make.shared to generate a shared file from a biom file
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:
[ERROR]: You are missing (
and when i saw the file, its empty. How can i resolve this issue ?
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?
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
Distributor ID: Ubuntu
Description: Ubuntu 12.04.5 LTS
You should upgrade your version of mothur, http://www.mothur.org/wiki/Download_mothur.