Error in core metrics results!

I have 12 samples sequenced, and when i made the core metrics analysis it was okay with 12 samples.But when i made some changes in the metadata ( i cancelled one sample and changed the ID of two samples, i repeated the core metrics analysis and i just found only 9 samples in all resulting charts, but the 3 missing samples have no relation with the samples which i cancelled and changed their ID’s!!!
Also, i repeated it for the third time and i found the same 9 samples except for weighted unifrac there were 12 samples exactly my samples!!!
So please any suggestion???

Hi @Soha,

My guess is that you are changing something else while modifying your metadata file. Hard to say what exactly.

Anyway, in my experience is much safer to filter your feature table or your distance matrix to remove the samples that you don’t want to use for other analysis. Additionally, this way you will not have to rerun all analysis within the core-analysis command but just the ones you want to redo.

In case you are wondering, for filtering check qiime feature-table filter-samples or qiime diversity filter-distance-matrix.

Hope this helps.

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