Chimeras detection in DADA2

[MiriamGorostidi (Miriam)]

Hello,

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,

[timanix (Timur Yergaliyev)]

Hi!

@MiriamGorostidi

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?)

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']

@MiriamGorostidi

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..

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.

Best,