[Bioperl-l] Next-gen modules

Peter biopython at maubp.freeserve.co.uk
Mon Jun 22 10:24:55 EDT 2009

On Wed, Jun 17, 2009 at 6:06 PM, Chris Fields wrote:
> Peter wrote:
>> Other issues to keep in mind:
>> (3) There should be no warning parsing files where the optional repeated
>> title is missing on the "+" lines (as discussed earlier on the BioPerl
>> list).
> Agreed, though we'll have to check the current fastq parser to see if that's
> currently the case.  I thought that was fixed but maybe not?
>> (4) When writing FASTQ files should BioPerl omit the optional repeated
>> title on the "+" line? Biopython omits this as I understand this to be
>> common practice, and can make a big different to file sizes - especially
>> on short read data from Solexa/Illumina.
> Agreed, particularly if it's commonly encountered.
>> (5) Also test reading and writing files with an optional description (as
>> well as an identifier) on the "@" (and "+") lines. See the NCBI SRA
>> for examples, e.g.
>> @SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
>> +SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
> Should be easy enough to implement with a simple regex.
>> (6) Test reading and writing files where the encoded quality string starts
>> with a "@" or a "+" character, e.g.
>> http://lists.open-bio.org/pipermail/bioperl-l/2009-May/029911.html
>> Peter
> Mark, getting all that? ;>
> chris

Another couple of points that I should have remembered earlier,
related to converting between PHRED scores and Solexa scores.
On the bright side, with Illumina abandoning the Solexa scores
in pipeline 1.3+, these issues will go away with time:

(7) If BioPerl will be converting Solexa scores to/from PHRED
scores as integers automatically (as discussed earlier), make
sure you round to the nearest whole number (don't just truncate
with a call to int!). MAQ does this by adding 0.5 before calling
int (while in Biopython I just use Python's round function).

(8) When asked to write out an old Solexa style FASTQ file,
what will you do if given a standard Sanger FASTQ file (or a
new Illumina 1.3+ FASTQ file) containing a base with PHRED
quality zero? This maps to a Solexa quality of minus infinity...
Right now the development version of Biopython will throw an
error in this situation, but mapping to the lowest observed
Solexa score might be reasonable.


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