[Bioperl-l] Next Gen Formats

Peter biopython at maubp.freeserve.co.uk
Fri Mar 12 05:06:46 EST 2010


On Fri, Mar 12, 2010 at 3:35 AM, Chris Fields <cjfields at illinois.edu> wrote:
> Ryan,
>
> We would have to see example files to get an idea of how feasible it is.
> You could possibly use a Bio::SeqIO::fasta and a Bio::SeqIO::qual
> stream, and interleave the two somehow.  However, BioPerl qual
> scores are PHRED-based by default, and I'm not sure how color-space
> data would work within that schematic.
>
> chris

Chris,

I am under the (possibly mistaken) assumption that PHRED scores
are used for SOLiD color space QUAL files - the key issue is each
score corresponds to the color call in the color sequence.

Ignoring color-space for a moment, are there BioPerl examples
of iterating over a pair of sequence-space FASTA and QUAL files?
i.e. What you'd get if you had a FASTQ file to iterate over.

[I guess Ryan could just merge the color-space FASTA and
QUAL into a color-space FASTQ file and iterate over that]

Peter



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