[EMBOSS] Conservation of FASTQ scores by the EMBOSS tools.

Peter biopython at maubp.freeserve.co.uk
Thu Sep 17 09:11:15 UTC 2009

On Thu, Sep 17, 2009 at 8:24 AM, Peter Rice <pmr at ebi.ac.uk> wrote:
>> Also, in contrary to what the documentation predicts, using the fastq
>> format for the output does not ignore the quality scores. (Not that
>> would be particularly useful, but…)
> This is deliberate. We have to write somethign in FASTQ format and we
> default to the fastq-sanger format. On input, fastq-sanger ignores qualities
> because there is no safe way to decide which format is correct.

So again, could you reconsider making "fastq" act like "fastq-sanger"?
The Sanger FASTQ format allows ASCII 33 to 126 for the quality scores,
a superset of the Solexa/Illumina FASTQ varaints - so even if you don't
know which kind of FASTQ file you have, and you don't care about the
qualities, parsing it as a Sanger FASTQ file will work.

Peter C.

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