Detecting FASTQ Quality Score Format

[bhan]

Hello,

I'm trying to determine whether FASTQ reads quality scores are encoded as phred64 or phred33. The naive method I came up with was to assume phred64 and then run through the entire FASTQ file and if any score is less than 64 then switch to phred33. However, I don't want to rely on this method in case I get high quality reads encoded in phred33.

Is there a better way to detect quality scores?

Thanks

[kopi-o]

If you run FastQC on your file, it will detect the encoding automatically.

Or you could try this Perl script:

https://www.uppnex.uu.se/content/check-fastq-quality-score-format

[bhan]

If you run FastQC on your file, it will detect the encoding automatically.

Or you could try this Perl script:
https://www.uppnex.uu.se/content/che...y-score-format

Ahh, you're right. I'll just extract it from the FastQC output, thanks!