What to do with Decontam Score QZA

I am trying to use Decontam for the first time in qiime2 to filter out contaminants. I used this code:

qiime quality-control decontam-identify
--i-table table_lily2_6neg.qza
--m-metadata-file metadata_lily.txt
--p-method 'combined'
--p-freq-concentration-column DNA_amount
--p-prev-control-column Species
--p-prev-control-indicator "blank"
--o-decontam-scores decontam_table_lily2.qza

This produced a decontam-scores file. Now that I have this, I do not know what to do to filter out the original frequency table. I think I need to use the 'qiime feature-table filter-features' function but I do not know what I would need to enter for the rest of the code to remove my contaminants. Would anyone be able to provide the code so that I can finish filtering my data?

Hi @liliez13,

After running decontam-identify you can visualize the decontam scores using the decontam-score-viz command to make sure that the threshold that is being used is appropriate for your data. It looks like in your above command you utilized the default 0.1 threshold.
After you have settled on a threshold you can run decontam-remove which will filter the feature table to remove the contaminant features for you, so no need to use 'qiime feature-table filter-features'

If you have any further questions please let me know!

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I did not know I had to run decontam-identify. Where would I be able to access code for both decontam-identify and decontam-remove. The decontam-scores code I use above is the only one that I was able to find and I was unaware that there was more to do.

You have already run decontam-identify above with the code in your first message.

The workflow for decontam within Qiime is as follows:

  1. qiime quality-control decontam-identify ; this command will run the decontam algorithm as seen above with a default threshold of 0.1 unless otherwise changed
  2. qiime quality-control decontam-score-viz ; this command will generate a .qzv file which can be vizualized here and will be a histogram of the decontam scores
  3. qiime quality-control decontam-remove ; this command will filter the feature table based on the scores in the decontam_score.qza file to remove contaminant features.

As for a more defined tutorial one has been generated and will go live once the latest updates to the Qiime Decontam functionality have been pulled into the main distribution.

I appreciate your interest in Decontam and I hope all that helps!

Thank you so much for your help! I appreciate it!

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