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renamed trace files

James Bonfield jkb at mrc-lmb.cam.ac.uk
Tue Oct 4 03:14:11 EST 1994

In article <MAILQUEUE-101.941003175523.480 at lcms-1.ncifcrf.gov> HUTCHISON at LCMS-1.NCIFCRF.GOV ("Don C. Hutchison") writes:
>    I have noticed that trace files from an ABI373A renamed with
>names different from those originally on the "sample sheet" (and
>converted to .scf files) cannot be displayed in xbap. Is there any
>way to get the trace file to display from xbap AND give it a
>different name?

A reading in 'Staden' format can include a header line describing the location
of the trace file. Bruce Roe mentions that the sequence and trace files must
have the same prefix. This is not necessary if the header line is correct. An
exact description of this can be found in doc/GelReadingFile.format, but I
summarise here:

        Format is ";%6d%6d%6d%-4s%-16s", where
        field 1 = total number of bases called
              2 = number of bases in the clipped sequence at the 5' end
              3 = number of bases in the sequence in this file
              4 = type of trace file.
                  "ALF " - Pharmacia A.L.F.
                  "ABI " - ABI 373A
                  "SCF " - SCF
                  "PLN " - Text only
              5 = name of trace file.

When outputting the sequence with ted you should use the 'include headers'
output style.

Once a sequence has been assembled into bap it is not trivial to rename the
trace file. The trace file name by then has already been stored in the
database. However it is possible to move all of the traces to a different
directory provided the RAWDATA environment variable is set to include this new


PS. Mail to staden at ... and news to bionet.software.staden are getting more in
sync (they were 5 days out at one time for us). However it's still the case
that things lag a bit. This can be seen by the fact that I've received Bruce
Roe's mail, but not as a news article. I prefer the newsgroup interface. Do
other people have this problem? (Address mail on that subject to me - not the
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 0223 402266   Fax: 0223 412282
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.

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