renamed trace files

Stefan Lundgren Stefan.Lundgren at cellfo.slu.se
Tue Oct 4 04:28:16 EST 1994


On 3 Oct 1994, Don C. Hutchison wrote:

> Staden-users,
> 
>     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?
> 
> Don Hutchison
> 
Hello there.

Although Professor Roe did a nice answer i would like to add some small
comments.

1st. It is possible to rename files. We do it all the time, as the ABI 
insists on adding spaces to it's filenames. It is most practical to have 
same name but this is not needed. (Using header output from ted)  But it 
is a good practice!

2nd. When you strip the cromatogram file making it into one in .scf format
you need to fix your seq file. Using ted and output. In the output file if
you use 'header' and not plain the output file will include info about the
cromatogram, and its format. (As well as secret and hidden sequences.)

The result file looks like this:
;   748    15   284SCF m13-9.09
;<A-CT-CAA---GGAA 
<snip>              |    |
                format cromatogramfilename.

Which means rename first then make ted output. 
Or the output will still point to the old file.

3rd. The sequence is entered into the project the cromatogram is not.
No renaming after entering the seqs.. (ofcourse)

The cromatogram also includes a format statement so it should be possible
to have this recognition automated (hint to programmer..) However we have
not been able to have XBAP cromatograms in a subdirectory. They 'need' to
be in the project directory. Which ofcourse gets clobbered with time.
(Another  h.t.p.)

Happy sequencing, stefan.

o------------------------------------------------------------------------o
| Stefan Lundgren                                phone 46-(0)18-67 33 19 |
|Department of Cellresearch                      fax   46-(0)18-67 32 79 |
|Swedish University of Agricultural Sciences                             |
|Box 7055                                                                |
|750 07 Uppsala  Sweden                                                  |
|                                          Stefan.Lundgren at Cellfo.slu.se |
o------------------------------------------------------------------------o





More information about the Staden mailing list