Alf sequencer data

James Bonfield jkb at mrc-lmb.cam.ac.uk
Wed Jun 12 03:41:18 EST 1996

Craig Cary Wrote:

>We have recently installed the package onto our Sun with Xterminal 
>application. We have data generated from an Alf sequencer that was 
>transfer both in ALF format and Staden format.  I successfully got the 
>data split using alfsplit and a file of file names made.  When I enter 

We have noticed that there are problems with alfsplit recently and have
made a newer version available by anonymous ftp
(ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/<MACHINE>/alfsplit.gz), but I
suspect this isn't your problem. If you've got the files split, but
pregap doesn't process them correctly then I guess there are two
potential problems.

1. Alfsplit hasn't generated the correct files
	Try using the newer alfsplit?

2. The makeSCF program cannot read the ALF files.
	makeSCF is the first stage of pregap. It converts everything to
	the SCF format. Could you please try "makeSCF -alf file.alf >
	file.scf" and tell us whether it works? Can trev display the
	file.alf and file.scf files?

It will probably also be useful if we could have a sample of one of your
problematic alf files.

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 412282
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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