[Bioperl-l] Update of SeqIO:: fastq Module for PacBio
Fields, Christopher J
cjfields at illinois.edu
Thu Sep 20 12:08:21 EDT 2012
On Sep 20, 2012, at 9:30 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Thu, Sep 20, 2012 at 1:47 PM, Dan Nasko <dan.nasko at gmail.com> wrote:
>> I've recently begun working through some PacBio sequencing data
>> and it has been chocking up current bioperl FASTQ I/O modules.
>> Here are the problems I'm running into:
>>  PacBio will report quality scores up to 100 - I believe there's
>> an upper limit of 93 and the FASTQ parser will throw and error if
>> that's surpassed.
> How exactly? The 93 limit comes from the fact that the top printable
> ASCII character is '~', 126 - 33 = 93. Are PacBio joining in the game
> of redefining FASTQ encodings? An example would be very
>>  Very often PacBio will have one base sequences. e.g.:
>> If this one base sequence has a quality character of "0"
>> (quality score 15), shown above, I/O will throw the following error:
> I thought that BioPerl bug had been fixed... or maybe it was the
> very similar situation of a quality score using the zero character?
This should be fixed. Is this using the latest CPAN release? The latest code from GitHub?
More information about the Bioperl-l