Hi all. I doing my 16S analysis. There is a column named sample-id in my metadata file. Now my problem is that this column in not showing in any of my qzv files. For example, feature-frequency-filtered-table qzv file or taxa bar plot qzv or alpha rarefaction plots etc. All these files (qzv) have all the columns (which are present in my metadata file) except this sample id file.
As this column is not showing as result I have to face too many difficulties such as while transferring my qza file to R studio for some analyses or my own thesis as well where I need this sample id column. More importantly, for some analysis in R, i should have this sample id column (compulsory)
I have tried to troubleshoot this problem too many times but it is not happening. The pattern for my metadata file is same as the one showed in moving picture tutorial. It is not giving any errors but it is not showing this sample id column.
I have uploaded pattern of my metadata and a qzv file picture for your reference.
In that qzv file you can see all column except the sample id column.
It will be a great help for me if any one from this forum can help me in solving this issue. Many thanks
The 'sample-id' column not visualized in the qzv files is a developer choice, not an issue.
The assumption is that in most of the cases you will look at the data grouping the samples by one metadata information.
I expect that if you export the data within the qza (by using the qiime2 export function), in the resulting tables the sample-id column should be there. If you working with R, using Qiime2R package should get all much easier for you providing all the information.
If you want to see the per-sample data in the qzv files, you need to provide the metadata file with a further column which should work as alias for the sample id. In your case, you already got two (forward-absolute-path and reverse-absolute-path).
Hi @llenzi ,
Thank you so much for your detailed explanation and prompt response.
Actually, I am working on the gut microbiome analysis for the first time, it will be great if you can explain a bit more on your second point, where you have mentioned Qiime2R package.
I am using Qiime2R package, but this sample id column is missing in my data frame when I search for my column names in R. To solve this issue in R, I am think to add this column (sample-id) in my data frame. I have not tried this yet.
In fairness I am not an expert of Qiime2R, I would start from this tutorial:
I may have mislead also, (sorry for that) you still to import the metadata file in R by read.table() command, but you should be good to go!
When you say 'the column sample id is missing in your data' in which qza file are you looking for it?
Cheers
Luca
