How to determine the encoding method of quality score in a fastaq file?

Question

[octpus616]

As you know, there are two general standards for the sequencing quality of fastq files: Phred+33 and Phred+64.

I have a very old fastq file that was generated on Genome Analyzer IIx platform (FC-104-50xx). I am not sure about the score of this fastaq has it gone through some conversions, is there some simple way to infer from the fastq total whether his sequencing quality score is Phred+33, Solexa+64 or Phred+64

[shenwei356]

Try seqkit convert which converts FASTQ quality encoding between Sanger, Solexa and Illumina.

[octpus616]

Since this file has been generated for a long time, I'm not quite sure if it has undergone some kind of conversion, is it possible to test the encoding way?

[Pierre Lindenbaum]

see Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?

[octpus616]

yeah, its works, thanks

Answer 1

[Juke34]

You can use gaas_fastq_guessMyFormat.pl from GAAS

e.g. with conda

conda create -n gaas_env gaas
conda activate gaas
gaas_fastq_guessMyFormat.pl -i myfile.fastq.gz

[octpus616]

its also works, thanks