[Bioperl-l] Update of SeqIO:: fastq Module for PacBio
p.j.a.cock at googlemail.com
Thu Sep 20 10:30:07 EDT 2012
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?
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