[EMBOSS] ABI to FASTQ with seqret

[Peter]

On Thu, Jul 22, 2010 at 12:16 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Thu, Apr 22, 2010 at 6:01 PM, Peter Rice <pmr at ebi.ac.uk> wrote:
>>
>> On 22/04/2010 16:48, Peter Cock wrote:
>>
>>> Does this mean there is an updated seqret in a public repository where I
>>> can convert an ABI file to FASTQ taking the ABI basecaller's sequence
>>> and PHRED scores? I'd be interested to test that... or a patch against
>>> EMBOSS 6.2.0.
>>
>> It is in the latest CVS code and will appeart in the July release.
>>
>
> Hi Peter R et al,
>
> I've just compiled and installed EMBOSS 6.3.1 on Mac OS X, and had a
> go converting some ABI (extension .ab1) files from our in house sequencing
> service to FASTQ - so far all the examples give Sanger FASTQ quality strings
> of "!" (ASCII 33, PHRED quality zero) or Illumina FASTQ quality strings of
> "@" (ASCII 64, again PHRED quality zero).
>
> I remember you saying ABI files can have two sets of quality scores,
> so perhaps my files have one set all of PHRED zero?
>
> I tried to find some 3rd party example files via Google, for example on
> http://www.elimbio.com/sequencing_sample_files.htm they have a zip
> file http://www.elimbio.com/Forms/pGEM.zip containing one ABI file.
> The output of this is more interesting:
>
> $ seqret -sformat abi -osformat fastq  -auto -stdout -sequence
> pGEM_\(ABI\)_A01.ab1
> @pGEM_(ABI)
> NANTCTATAGGCGAATTCGAGCTCGGTA...GNN
> +
> "!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"!"...!"!"!"
>
> I truncated this for brevity. Here the quality string repeats ASCI 34, ASCI 33
> (PHRED quality 1, quality 0) which is rather strange. The sequence appears
> to agree with the provided file pGEM_(ABI)_A01.seq
>
> Have I just been unlucky with the AB1 files that I have looked at? Thus
> far all the quality scores seem meaningless.

I went back through my old emails, and see you had been testing with
http://www.appliedbiosystems.com/support/software_community/ab1_files.zip
(I had trouble downloading this with curl - Firefox worked). Looking at these
ABI files with seqret as FASTQ does seem to give meaningful quality scores.
Curious.

Peter C.