Identifying batch effect

Hi,

My 16S data was sequenced in 2 different runs.I have separately denoised them using same parameters.Is it good to merge table & rep seqs artifacts from both runs & then do taxonomy classification?I want to export these data into R & then identify batch effect using some stastical test.My sample ids contain batch info,thus are unique.

Thanks in advance
Tahseen

I’m not an expert on this stuff, @Tahseen_Abbas, but that sounds like a reasonable approach to me.

Especially this:

:smile:

As a bonus, if you have a sequencing run column in your metadata, you can get some quick qualitative insight into batch effect by running core-metrics or core-metrics-phylogenetic and viewing the Emperor plots produced. Coloring those plots by sequencing run can help you visualize how batch impacts beta diversity.

Best,
Chris :goat:

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