Does a metadata file have to be provided to create a biom file, for subsequent analysis of beta diversity in Phinch?


I am currently using the Galaxy Europe platform to analyze 16S sequencing data, while using the 16S Microbial Analysis tutorial ( I have reached the step where the shared output file is combined with the mouse metadata file (i.e., mouse.dpw.metadata) to create a biom file, which is subsequently used in Phinch to examine beta diversity.

From my reading, it appears that the metadata provides additional technical details about the samples (e.g., day of collection). This information can be included with the output data generated in Galaxy to form the biom file. I modified the mouse.dpw.metadata to include my samples and the days that they were collected. However, I received an error when I used the make.biom tool and included this modified file.

I was able to proceed without using the metadata file. However, I was wondering how the Phinch program takes the metadata into account? For instance, the taxonomic bar chart that is produced in Phinch does not include information on the sampling days. As a result, I’m wanted to reach out to gain a better understanding of the purpose of the metadata file and whether it is important to include in the 16S sequencing analysis.

Thank you for your time and I look forward to hearing from you. Have a wonderful day!


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Welcome @Erica_Dasi

The answer is probably yes, otherwise you won’t be able to filter down to specific groups of samples with Mothur tools or later Phinch itself.

Where is “metadata” used?

The metadata input sets allow you to filter using the “groups - Groups to include” option on the Make.biom tool form.

The parsed metadata information is also then included in the final biom dataset output later input to Phinch, where it can be utilized/filtered on when using that tool.

Why is your metadata file failing?

There is probably a format problem. Extra spaces, etc can cause problems. The data should be tab-delimited, each column’s label/data needs to be formatted correctly, and the file should not contain any extra lines. The header also needs to be correctly formatted. How to check for format problems like this are similar to the help in this post.

More help: