[Bioperl-l] Creating a fastq format file?

Joel Martin j_martin at lbl.gov
Fri May 15 13:44:34 EDT 2009

> The wikipedia FASTQ page [5] says that "Sanger format encodes a Phred
> quality score from 0 to 60 using ASCII 33 to 93." It generally
> accepted that Phred qualities are limited to 60. See column 5
> (sa6(ASCII)). Or are there exceptions?

consed and phrap reserve values 98 and 99 to mean user edited bases.
disallowing those would probably cause trouble eventually, as consed
reads fastq files now.


On Fri, May 15, 2009 at 03:39:55PM +0200, Heikki Lehvaslaiho wrote:
> Sorry for confusingly composed post. Here is  a cleaner version.
>    -Heikki

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