How does FASTQC work?

Question

[Irvin]

Hello,

I'm relatively new to using FASTQC and was wondering how it works and how it determines the quality of a read. The documentation doesn't mention much and is more of an instruction manual. Thanks.

Answer 1

[GenoMax]

new to using FASTQC and was wondering how it works

Have you looked at these pages: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/ They provide information about individual modules.

[Irvin]

Yes these pages popped up when I read the documentation but I was confused. Do they mean that the .fastq files all have quality information encoded within the file already?

[Pierre Lindenbaum]

https://en.wikipedia.org/wiki/FASTQ_format#Quality

[GenoMax]

Do they mean that the .fastq files all have quality information encoded within the file already?

Yes they do. Each base has a corresponding quality call in fastq record.

As @Pierre noted you will find it useful to check the entire Wiki Page for Fastq format: https://en.wikipedia.org/wiki/FASTQ_format

[Irvin]

Got it. Thank you!

[igor]

Do they mean that the .fastq files all have quality information encoded within the file

The Q is for quality.

Answer 2

[Pierre Lindenbaum]

Hum your question is not clear to me...

how it works

it scans all the reads and makes statistics

how it determines the quality of a read.

https://en.wikipedia.org/wiki/FASTQ_format#Quality

see also: https://hbctraining.github.io/Training-modules/planning_successful_rnaseq/lessons/QC_raw_data.html

[Irvin]

Ah so the .fastq files contain quality information. Thanks!