[Bioperl-l] FASTQ support in Biopython, BioPerl, and EMBOSS

[Chris Fields]

On Jul 27, 2009, at 6:51 AM, Peter wrote:

> On Sat, Jul 25, 2009 at 8:50 PM, Chris Fields<cjfields at illinois.edu>  
> wrote:
>>
>> From this it could be summarized that converting to sanger format  
>> is least
>> problematic, as possible issues may be encountered when converting  
>> to the
>> other variants.  We'll need to fix the solexa quality calculations  
>> in the
>> BioPerl parser as noted in your previous post; I'll work on that.
>>
>
> BioPerl SVN (revision 15887, just updated on the off chance you
> have committed any fixes recently) also has a problem going the
> other way (from FASTQ Sanger to FASTQ Solexa),
>
> $ more sanger_faked.fastq
> @Test PHRED qualities from 40 to 0 inclusive
> ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN
> +
> IHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
>
> $ perl bioperl_sanger2solexa.pl < sanger_faked.fastq
> @Test PHRED qualities from 40 to 0 inclusive
> ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN
> +Test PHRED qualities from 40 to 0 inclusive
> hgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFEDB@><
>
> Depending on your email viewer this may not be obvious, but
> the sequence line is length 41 but the quality line is only 40
> characters. And again, I also suspect a problem in the mapping
> itself.
>
> Peter

I added this (and the others) to our ticket tracking this.  Looks like  
solexa conversion either way is borked, which is very likely an issue  
with conversion.

chris