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. -- DSM Nutritional Products AG R&D Human Nutrition & Health Bioinformatics - Bldg. 203.4 / 188 P.O. Box 2676 CH-4002 Basel / Switzerland Tel. +41 61 815 8264 > -----Original Message----- > From: emboss-boun...@lists.open-bio.org [mailto:emboss-boun...@lists.open- > bio.org] On Behalf Of Peter > Sent: Donnerstag, 22. Juli 2010 15:14 > To: Peter Rice > Cc: emboss@lists.open-bio.org > Subject: Re: [EMBOSS] ABI to FASTQ with seqret > > On Thu, Jul 22, 2010 at 1:28 PM, Peter Rice <p...@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 > _______________________________________________ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately. _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss