Obtaining Q30/Q60 Values from Fastq Files

Question

[joe_genome]

Hello,

I've run FASTQC on my FASTQ files and would like to extract the Q30/Q60 (Phred) Quality Scores. Does FASTQC provide this information directly, or do I need to calculate it separately? I'm unsure how to retrieve this information. Any guidance would be greatly appreciated!

Answer 1

[GenoMax]

would like to extract the Q30/Q60 (Phred) Quality Scores

and

do I need to calculate it separately? I

As in average (which does not make a lot of sense) for the entire dataset?

Fastq format encodes scores for each base in the record for every sequence in a position that corresponds to the sequenced base. Q60 scores appear to be valid only for PacBio HiFi data otherwise max for Illumina is in the Q40-Q43 range.

[joe_genome]

thanks that makes sense! thanks for sharing the link!