when to filter chloroplasts and mitochondria from our table.qza and rep-seq.qza

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1

hi
I checked my taxonomy barplot, there, chloroplast and mitochondria are present. So I have removed those. but I am thinking this I should have removed before alpha and beta diversity analysis.
Is it so?
when should we exactly filter these contaminants?

2

Hi!
It is better to remove them (of course, if you are not interested in them) before any analysis from table.qza since they can really affect the results.
No need to filter rep-seq.qza

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3

hi
but we should also remove these from rep-seq file because we are also using the same.

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4

We are using them, but all calculations are performed on the data in table.qza. Rep-seqs should contain all id’s from table.qza, but it’s not bad if you have data in rep-seq.qza that are not in table.qza anymore

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6

again I got one doubt.
taxonomy.qza file that we are using for filtering out contaminants. and generating a new table and that table we will use for further analysis.
and when you come to the taxonomic analysis, again generating taxonomy.qza file and proceed.
Isn’t it so confusing?

7

Usually I perform taxonomic analysis before any other analyses, after I obtain all necessary files. Then I filter my tables, including removing of mitochondria and chloroplasts, then I perform the rest of analyses, using already created (before filtration) rep-seq and taxonomy files.

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