I am a student, just getting familiarized with sequencing analysis, so I am not even sure if I am asking the correct question, but here it goes:
I have a set of sequences from a lake, obtained on different holidays. There are 7 different timepoints across 3 holidays (and one control), with each timepoint containing numerous replicates. Each replicate is its own sample ID.
I am trying to group all of the replicates together, and I have used the feature-table group function to do this (using the mean ceiling method).
The question is how do I take this new grouped table and obtain visualizations with it?
For instance, when I try to summarize this table, the metadata file does not match, and I get the following error:
Plugin error from feature-table:
The following IDs are not present in the metadata: ‘ID2’, ‘ID6’, ‘LD3’, ‘LD7’, ‘MD1’, ‘MD5’, ‘NA4’
Debug info has been saved to /tmp/qiime2-q2cli-err-lw2476hf.log
Will I need to make a new metadata file? And if so, how exactly does feature-table group rearrange these samples? For instance, will the new metadata file need to only contain 7 rows, one each for the samples listed above in the error? And will the barcodes column need to be taken out or does this matter?
Welcome and all questions are welcome!
Thanks for providing the design of your project. Just want to confirm that when you say
You are referring to technical replicates and not biological replicates, correct? If these are technical replicates then your approach is correct and your new table can be used just as as you would with your old feature table. The only thing that would change, as evidence by your error message, are the new assigned IDs.
From the feature table group plugin page:
--o-grouped-table ARTIFACT PATH FeatureTable[Frequency]
A table that has been grouped along the
given `axis`. IDs on that axis are replaced
by values in the `metadata` column.
[required if not passing --output-dir]
This says that once you have merged your replicates they will be assigned a new sample ID which is the value from the categorical column used to merge them. So you’ll need to modify your metadata file to include these new IDs instead of the your former SampleID because they no longer exist in the new feature-table. The barcodes columns at this point doesn’t really matter so they can be taken out or kept in without any consequence. Let us know if this solves your issue.
Ahhh. Thank you for the reply. They are biological replicates, unfortunately. Do you know of any way to do this with biological replicates?
If these are biological replicates then you don’t need to worry about grouping them since we need each replicate separately to be able to perform downstream analyses.
As long as you have the appropriate columns in your metadata file describing these move on with your analysis. Following along the Moving Pictures tutorial shows a good example of the workflow you could easily follow.
Will do. Thanks a lot for your replies!
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.