about dada2 filterandTrim parameter

[chulghim]

Can i get how to determine dada2 filterAndTrim() paramer? (truncLen=c(240,230), minLen=200, maxN=0, truncQ=2, maxEE=c(2,5) ..)

For example: Illuminia MiSeq - (2*250bp reads) 321F: TAATTCGTCCTACGGRAGGCAG 800R: AGCCGGACTACCRGGGTAT

I am curious if there is any formula.

[ycl6]

There isn't a formula I'm afriad. The paramter you would most likely need to alter from the default values is truncLen. You need to inspect the quality plot that you generate with plotQualityProfile to judge how many bases you would keep and at the same time not truncating the reads too much and end up unable to merge majority of the paired read, i.e. you need to have a general idea of what's the length distribution of your amplicons

[chulghim]

Thank you very much. That's what i want to know.

Best regards, Namchul.

2020년 8월 10일 (월) 오후 5:19, I-Hsuan Lin notifications@github.com님이 작성:

There isn't a formula I'm afriad. The paramter you would most likely need to alter from the default values is truncLen. You need to inspect the quality plot that you generate with plotQualityProfile to judge how many bases you would keep and at the same time not truncating the reads too much and end up unable to merge majority of the paired read, i.e. you need to have a general idea of what's the length distribution of your amplicons

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[ycl6]

@chulghim Glad to help, I'll close this for now