batch data analysis

[James Doonan]

I have been using the PacBio CCS Amplicon SOP v2 (qiime2 2022.2).

I used this SOP up to and including step 4.4 to create an OTU abundance table with taxonomy information. I have new samples that I want to add to the analysis. Is there a way to analyse the latest samples and integrate the old and new data output using the same SOP? Or should I analyse the combined dataset?

Thanks,

James

[Andre Comeau]

James,

Sometimes opinions vary on whether to always reanalyze all together or to keep separate and merge at the end...in the case of new data from a separate sequencing run (as assumed this would be; esp. if older Sequel2 data we generated with new Vega data you'll get from us from now on), it might be a good idea to analyze/run the pipeline separately and then merge your feature table at the end (there are specifically QIIME2 commands that allow you to do this), making sure to include an extra column in your merged metadata file that indicates which sequencing/analysis run each sample was on so that you can double-check your PCoA plots (for example) for any sample grouping coming from the separate runs. 

 

	ANDRÉ M. COMEAU, PhD Manager • Integrated Microbiome Resource (IMR) T: 902.494.2684 | E: andre....@dal.ca	​Address for deliveries: Dept. of Pharmacology Tupper Med. Bldg., room 5D Dalhousie University 5850 College St. Halifax NS B3H 4R2
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From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of James Doonan <clydea...@gmail.com>
Sent: Tuesday, June 10, 2025 8:34 AM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: [microbiome-helper] batch data analysis

 

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