[EMBOSS] SCF files (Staden)

[Tom Keller]

Greetings,
You can use BioPerl for this. EMBOSS and perl work well together.
Here is a link: http://www.bioperl.org/wiki/HOWTO:SeqIO

cheers,
Tom
MMI DNA Services Core Facility
503-494-2442
kellert at ohsu.edu
Office: 6588 RJH (CROET/BasicScience)

OHSU Shared Resources






On Nov 29, 2011, at 9:36 AM, Peter Rice wrote:

> On 29/11/2011 17:13, Peter Cock wrote:
>> Dear all,
>> 
>> I am hoping to convert some ABI "Sanger" capillary files
>> into SCF (i.e. *.ab1 to *.scf), and currently I've installed
>> the Staden io_lib just to get their convert_trace tool.
>> 
>> Does EMBOSS support SCF files as defined here:
>> http://staden.sourceforge.net/formats.html
>> 
>> I presume these are different from the "Staden" format mentioned here:
>> http://emboss.sourceforge.net/docs/themes/SequenceFormats.html
> 
> "Staden" is GCG's text only staden format with an id in angle brackets. 
> We also support experiment format.
> 
> I'm looking into formats now - I'll add SCF if I can do it before Xmas.
> 
> regards,
> 
> Peter Rice
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