XBAP and Abi trace files?

Bonfield James jkb at mrc-lmb.cam.ac.uk
Tue May 30 04:28:38 EST 1995

Walter and Adrie wrote:

>Hello Staden programm users,
>We have a problem with loading trace files from our recently operational Abi
>sequencer into Xbap running on a Silicon Graphics computer.
>After opening a database we can not load an Abi-file. The next message
>appears: error in arrfin: too much data.
>With the program TED everything works well.
>Any help on this subject will be appreciated.

I suspect you are attempting to input the binary ABI trace file to xbap. Xbap
only supports textual sequence formats so you'll need to extract the sequence
from the ABI file first. I suggest you either use prebap (see
$STADENROOT/src/scripts/prebap/Manual) or use trace2seq and vep by hand if
you're only assembling a few reads.

To use trace2seq you need to type something like:

trace2seq -ABI "Sample 01" -output "reading"


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.

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