[Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO

Peter biopython at maubp.freeserve.co.uk
Sat Jul 10 07:43:47 EDT 2010


On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap <abhishek.vit at gmail.com> wrote:
> Hi (Chris)
>
> I feel I might be hitting a bug or missing something. I am trying to convert
> a raw FASTQ from ASCII-64 to ASCII-33.  I am copying the actual code and IO
> for more clarity. I think the quality line is missing and the read is
> breaking into two lines.
>
> Any obvious mistakes ?
>
> Thanks!
> -Abhi

It looks like you are getting FASTQ out rather than FASTQ (notice in addition to
missing the qualities, the record starts with ">" rather than "@".
Strange, as you
do seem to be using the right FASTQ format and variant names. You could try
using format="fastq-sanger" and format="fastq-illumina" rather than
setting variant,
to see if that changes anything.

Peter



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