ABI 377 vs. 3.0 trace file display problems on trev

James Bonfield jkb at mrc-lmb.cam.ac.uk
Fri Apr 11 02:49:55 EST 1997

Ilkka Havukkala wrote:

>recently we have seen increased amounts of trace files that display ok
>on the ABI software (for 377, vs. 3.0), but on STADEN in trev display
>with problems. STADEN version is 1996.1. (Will soon try vs. 1996.2 to
>see if the problems persist there.)

We've had the odd report of problems, but so far have never received an ABI
file that trev couldn't accurately display (that the ABI software could).
Could you please uuencode and email me a representative set of the problem
traces? We can then try to find and fix the problem. I don't think we've
got a hope in fixing them without the traces to play with.

>1) electropherograms which show gibberish characters above the traces in

I've seen this for edited traces. It appears that editing on the ABI
software writes out a slightly different format ABI file, that we cannot
understand. Is this likely to be a problem?

>2) electropherograms which show only one colour of traces, sequence
>above is ok
>3) electropherograms which show sequence ok, but get gradually out of
>alignment from the trace peaks, at 300 bp plus already 3-5 basepairs.

I've never heard of these. It'd definitely be good to see the traces.

>There is now difference in the MacX X-windows displays
>and the native Sun unix X-windows displays in this respect.

Is this really the case - that trev displaying to a Sun X server works
differently than to a Mac X server? Even when running the same trev binary?
If so, which is the system that displays wrongly. It sounds like an X
server bug, as both X servers should display identically and trev doesn't
"know" where it's display is.

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
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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