[Bioperl-l] Next-gen modules

Peter biopython at maubp.freeserve.co.uk
Wed Jun 24 10:56:13 EDT 2009

On Wed, Jun 24, 2009 at 12:48 PM, Peter Rice<pmr at ebi.ac.uk> wrote:
> I was planning to suggest a get-together at BOSC in Stockholm so we can
> identify common cross-platform issues. I'm sure there are many ways we
> can conform with naming and interfaces and perhaps even share code.

That would be a good idea - but while there are quite a few Biopython
people at BOSC this year, I don't know if there will be many from BioPerl
(there isn't a BioPerl update talk scheduled).

>>>>> We also allow the integer quality score format ... is anyone still
>>>>> using that (it looks horrible to me :-)
>>>> Do you mean the QUAL file format holding PHRED scores?
>>>> Roche provide tools to turn their SFF files into FASTA and
>>>> QUAL files, so they are still used.
>>> Probably ... unless there is a Solexa version too.
>> We may be talking at cross purposes here, this is QUAL format:
>> http://www.bioperl.org/wiki/Qual_sequence_format
> Yes that is different. We'll worry about separate QUAL files later (we
> already find separate GFF files a pain for features) and still with the
> "fastqint" format name.

So when you say "fastqint" are you talking about something else?
Could you show us an example record in this format?

[I need to remember to proof read my evening emails more carefully]

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