About Quality filtering

[zwfsnowdream]

I have a question that I am a bit confused about and would like to ask for clarification. I would like to know if the default values for the parameters Minimum single bp quality and Minimum average read quality are set to 0, meaning that base quality is not filtered when analyzing indels and substitutions. In this case, would the analysis results be accurate, especially when applied to base editor analysis?

[kclem]

Hi @zwfsnowdream,

If you sequencing is high quality, you shouldn't have to use these filters to get accurate base editor analysis. If you see a lot of substitutions throughout your amplicon, you may want to add these quality filters. You can also check your base quality with fastqc