qiime2 import (how to convert data from excel to biom)


I am using Windows 10 and using Ubuntu 20.04. I want to import my data. I have taxonomic data as shown below using 16S sequencing.

Also I have metadata in excel sheet (separated into intervention and control group in each sheet) as shown below.

As you can see it is all formatted with excel sheet, and I know I have to convert excel to biom format. Can you help me how to create biom format? I have tried biom convert from other forum questions, but it did not work because I am not sure 1) where to place my data and 2) how to convert this.

Based on my understanding, I think I have to place this file to the directory that is connected to qiime2, not in my local computer file. But I don't know how to locate my directory and how to place my file in that directory, then how to convert it to biom format.

Can you walk me through the process in detail as I am savvy to these software or programming?

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Hi Choa,

I'm not a mod on the forum, but I'm not aware of a way to go directly from Excel to Biom format. If you save your file as a tab delimited file (as simple as File -> save as -> Choose "tab delimited .txt" in the file type) you should be able to run the biom convert command you attempted in your screenshot.

As an aside, the error you're getting is saying that the file doesn't exist, meaning it can't find it. So just watch your filenames and make sure that it matches your file/is spelled correctly and that you're in the same folder as the file. I generally make a new directory for each project I work on and then run analyses from there. Once QIIME is activated (like it is in your screenshot) it will work from any directory. If using the terminal is confusing, you can open a File Explorer window and look at the filenames/locations that way.

Hope that helps,


Hi Samantha,
Thank you for your response. I am not sure how to place my file to my directory. For example, my file is under C:/Users/apf_temp_admin/share (as shown below). How can I work my file on a new directory I make? Or can you help me what command line I can run in my terminal? Thank you!

Hi Choa,

Moving files to different directories (i.e. folders) works the same way as it would if you were moving any other non-qiime2 related file. You simply click and drag the file into the new directory. Or right click on the file and choose the move option.

To do so in the command line you can make a directory with mkdir and move or copy files with mv or cp respectively. Here is a cheatsheet that I give to folks who are new to command line. You might want to read up/watch YouTube videos on command line architecture/usage to get the basics down.

I haven't watched this, but it looks promising. Linux Command Line Tutorial For Beginners 1 - Introduction - YouTube



Thank you so much! Those videos did help a lot!

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