On Wed, Sep 16, 2009 at 7:57 AM, Charles Plessy <[email protected]> wrote: > > Dear EMBOSS developers, > > I have multi-sequence file in FASTQ format that contains sequencing reads, and > would like to retreive them the with seqret. But as you see in the following > example, quality scores are not preserved: > > $ seqret P13-CA.fq:F1EZY7316JY25B fastq::stdout > Reads and writes (returns) sequences > @F1EZY7316JY25B rank=0000040 x=3973.0 y=285.0 length=68 > AATGATACGGCGACCACCGAACACTGCGTTTGCTGGCTTTGATGCACTTCTCATGGCCAATTTCATTG > + > """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
You need to use "fastq-sanger" (or the other variants), since in EMBOSS, "fastq" currently means FASTQ ignoring the qualities. This is documented: http://emboss.sourceforge.net/docs/themes/SequenceFormats.html As an EMBOSS user, I think the current situation is confusing, and it would make much more sense to have "fastq" just an alias for "fastq-sanger" (which would be consistent with Biopython and BioPerl). http://lists.open-bio.org/pipermail/emboss-dev/2009-July/000576.html And also this email - especially the last example: http://lists.open-bio.org/pipermail/emboss-dev/2009-July/000599.html > The purpose was to use seqret as a workaround for the fact that > vectorstrip does not keep the quality either. That's also been suggested, and is likely to be supported in future. http://lists.open-bio.org/pipermail/emboss/2009-August/003722.html Peter _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
