Chimeras detection in DADA2


I would like to know if performing DADA2 step without the --p-chimera-method parameter would be actually removing chimeras (since --p-chimera-method default value is 'consensus', right?)

I have been running this step without that parameter and I would like to know if they have been removed or not.

Moreover, as I am a computer scientist and don't have much biology knowledge, I would like to know how I could answer my lab colleagues about the % of chimeras found in each experiment..

Thank you so much in advanced,


Right, as it stated in the plugin desription:

"consensus": Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed. [default: 'consensus']

Prior chimeras removal there are several steps under the hood which remove some of the reads based on the length, quality etc. So, if you are specifically interested in the % of chimeras (not in the % of "good" reads from the input), I would substract "non-chimeric" counts from "merged" and convert the difference to the % from "merged", so you will get % of chimeric reads from reads, successfully passed all the filters (except chimeras removal) and merged.


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