Multiple lane runs on MiSeq of the same samples to get deeper sequencing depth. How to combine?

Hello, I am somewhat new to bioinformatics and qiime2. I 16S sequenced 243 samples over 3 MiSeq lanes and now have 3x reverse and forward reads (paired end) for each sample. The goal of sequencing the same samples over 3 lanes was to increase sequencing depth. What is the best way to combine this data?

I see on this forum that I could create a script to combine all my fastq.gz files with the cat command. For example, I would do:

cat /A/NF7_PP_S84_L001_R1_001.fastq.gz /B/NF7_PP_S84_L001_R1_001.fastq.gz /C/NF7_PP_S84_L001_R1_001.fastq.gz > NF7_PP_S84_L001_R1_001_merged.fastq.gz

where A, B, and C directories are the 3 seperate MiSeq lane runs and the sample is NF7_PP. However, in the linked forum question above, someone mentioned that you can also combine samples downstream in the analysis. I am looking for guidance on what the best thing to do is. The forum mentioned that doing the combining downstream would help test for batch effect but at what point would it be combined?

I thought I could make a table.qza for each run (so I would have 3 tables) with qiime dada2 denoise-paired then use qiime feature-table merge to "merge" all the tables. When I tried this method, there was an error:

Plugin error from feature-table:
Same samples are present in some of the provided tables: TM9-I, NF8-PP, NM1-G, RM3-E...

Which doesn't make sense to me because I thought it would use the sample IDs to merge them all together. What is the best way to go about this? I'm not fully understanding everything being said in the linked forum so I apologize if my question was already answered. Thank you for your time.

Hello @Bark9299,

The error you're seeing is because the default value for the --p-overlap-method parameter is error_on_overlapping_sample. It sounds like the sum option may be the one you're looking for.

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