What about chloroplast, mitochondria and plant contaminants?

[khaknasheen]

Dear Researchers,

I have thoroughly studied Qiime 2 for dummies tutorial. When I come across the conceptual views of workflows, I noticed and thought about the contaminants such as chloroplasts and mitochondria in 16S and plant materials in ITS. After importing raw sequences to Qiime 2, then demultiplexing and denoising, we get a feature table and representative sequences. However, the feature table and representative sequences could not 100 percent feature table and representative sequences because of the presences of some plant related sequences and contaminants like chloroplast and mitochondria. Now my question: Is there any workflow so that I remove the contaminants and plants materials before reaching to feature table and representative sequences so that my feature table and sequences only contain bacteria and fungi, not other contaminants? . I would be very thankful if any researcher would help me and provide me with a workflow so that I reach to feature table and representative sequences safely!

Regards,

[Mehrbod_Estaki]

Hi @khaknasheen,
In the tutorial you are referring to, there is a line tucked away at the end of this section which reads:

1. Filter your feature table and representative sequences ( FeatureData[Sequence] artifact) to remove certain taxonomic groups. This is useful for removing known contaminants or non-target groups, e.g., host DNA including mitochondrial or chloroplast sequences. It can also be useful for focusing on specific groups for deeper analysis. See the filtering tutorial for more details and examples.

I think this and the link it provides might be what you are looking for?

[khaknasheen]

Dear Researcher,

Thanks. Solved!