Question

MultiQC real threshold in every parameter

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3.7 years ago

jimmy0958073736 ▴ 40

Hi everyone I have a curious question about the MultiQC threshold. Once we analyze Fastq data with FastQC and MultiQC, it will plot some figures with some of the characters (e.g GC rich, N content, quality score...) and also the statements which let you know whether passes the threshold or not. I want to know the exact number of upon characters (e.g. GC < 40% or quality score >30 means pass). So how can I get it and also the citation?

MultiQC FastQC RNA-Seq quality control • 1.3k views

ADD COMMENT • link updated 3.7 years ago by GenoMax 147k • written 3.7 years ago by jimmy0958073736 ▴ 40

score 0 · Answer 1 · 2021-03-03

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3.7 years ago

GenoMax 147k

FastQC uses a configuration file called limits.txt that defines the limits used for various plots/tests. You can find that file in Configuration folder in FastQC distribution. This file determines the FastQC results which are parsed and plotted by MultiQC.

MultiQC uses plotting functions that are described here (LINK).

ADD COMMENT • link 3.7 years ago by GenoMax 147k

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So amazing answer. THX But did the limitis.txt based on any journal or citation? Or even I can adjust the parameter anytime?

ADD REPLY • link 3.7 years ago by jimmy0958073736 ▴ 40

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Those values are based on ranges for normal genomic sequencing. You can edit the file to make changes. It is even possible to use a custom limits file with --limits option at run time.

ADD REPLY • link 3.7 years ago by GenoMax 147k

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Got it. Thanks for giving me a big help.

ADD REPLY • link 3.7 years ago by jimmy0958073736 ▴ 40