[EMBOSS] ABI to FASTQ with seqret

[Chevreux, Bastien]

AFAIK ab1 files do not have phred quality scores included. At least they did not a couple of years ago.

You need to mangle them through a basecaller (TraceTuner, phred, others) to get these scores.

B.

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> -----Original Message-----
> From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-
> bio.org] On Behalf Of Peter
> Sent: Donnerstag, 22. Juli 2010 15:14
> To: Peter Rice
> Cc: emboss at lists.open-bio.org
> Subject: Re: [EMBOSS] ABI to FASTQ with seqret
>
> On Thu, Jul 22, 2010 at 1:28 PM, Peter Rice <pmr at ebi.ac.uk> wrote:
> >
> > On 22/07/10 12:22, Peter C. wrote:
> >
> >>> 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.
> >
> > There are two sets of quality scores in that file. Both are the
> > alternating characters 1 and 0. Adding 33 gives the scores you see.
> >
> > Looks as though EMBOSS is just reporting what it finds.
> >
> > The file offset is the value returned by function
> > ajSeqABIGetConfidOffset. It simply reads one byte from there for each
> > base of sequence length.
>
> Looks like that particular random example from the internet was just odd.
>
> >> 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.
> >
> > It should look for a PCON tag in the file and pick up the second of two,
> > or the first if there is only one.
> >
> > Can anyone on the list enlighten us further on what is intended for the
> > quality socrss in these example files?
>
> The gGEM example I have no idea - I just found it with Google.
>
> I can send you a couple of our locally produced AB1 files off list
> if you wouldn't mind having a look at them. It may be that however
> these are being generated there simply are no useful scores inside.
>
> Peter
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