On Thu, Jul 22, 2010 at 12:16 PM, Peter <biopyt...@maubp.freeserve.co.uk> wrote: > On Thu, Apr 22, 2010 at 6:01 PM, Peter Rice <p...@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. _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss