about how to use staden!!!

Simon Andrews simon.andrews at bbsrc.ac.uk
Thu Aug 9 04:05:10 EST 2001


"¡¡Ryan" wrote:
> 
> hi,all,
> 
>       Thanks for your advice. I have got the staden package. But I can`t
> open any files in GAP4 viewer. It only can open *.aux files. How can I
> change the ABI files to *.aux files?

You need to use the pregap4 program to process your ABI files into .exp
files.  This also allows you to mask any vector you might have present,
and any poor quality sequence.  You then bring the .exp files into
Staden using the "Assembly -> Normal Shotgun assembly" command.  The aux
files are the completed assembly. A single aux file can contain
information about thousands of individual traces in an assembly.

Gap4 is an *assembly* viewer, it is only useful for assembling sequences
and viewing the contigs (and allows you to refer back to the traces at
that point).  If you just want to look at an individual trace file, and
not do anything else with it then use Trev (which is also part of
Staden).

The documentation for Staden is here;

	http://www.mrc-lmb.cam.ac.uk/pubseq/documentation.html

Simon.




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