[EMBOSS] Convert scf to fasta

Tiandao Li litd99 at gmail.com
Mon Apr 26 15:48:56 UTC 2010

Yes, definitely try phred/phrap/consed for base calling in batch mode, just
store all scf files in one folder, and google some help for it. the result
files include fasta files with quality scores, it is aonvient for downstream



On Mon, Apr 26, 2010 at 8:29 AM, Fernan Aguero <fernan.aguero at gmail.com>wrote:

> On Mon, Apr 26, 2010 at 9:47 AM, Philip H. Jones
> <p.h.jones at liverpool.ac.uk> wrote:
> > Hi
> >
> > I have a large number of .scf files that I need to batch convert to fasta
> > format. I thought that abiview would be able to perform this function but
> I
> > cannot get abiview to read the .scf files (although various sources on
> the
> > internet suggest that it should be able to do so). It reads and displays
> > .ab1 files with no problems. The webpage describing input formats
> > (http://emboss.sourceforge.net/docs/themes/SequenceFormats.html) doesn't
> > mention scf. Is there an EMBOSS application that would convert .scf to
> .fa?
> > Any help would be greatly appreciated. I am running Mac OSX 10.5.8 with
> > EMBOSS 6.1.0-4 installed via fink.
> >
> > Best wishes,
> >
> > Phil Jones
> AFAIK, abiview reads trace files but it displays the trace and
> sequence data _graphically_. That is to say it's not really meant to
> be used for batch conversions.
> For this you may want to try phred (free for academic use, see
> www.phrap.org, runs on many Unix flavours) or any other basecaller
> (don't use OS X myself, can't provide more info on this).
> E.g. if you have all your scf files in a directory called 'chromats'
> you would run phred like this:
> phred -id chromats -sa my-sequences.fasta
> to get a multiple fasta file named 'my-sequences.fasta' with the
> corresponding sequences.
> Note that you have many more options, as phred will also export/report
> base quality values for your sequences.
> Cheers,
> --
> fernan
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