Phred argument in Staden

Pinar Kondu pkondu at attbi.com
Thu May 15 03:13:34 EST 2003


Malcolm, thanks for your phone support!
Just for the record, I am trying to understand the use of the mutation
detection program. I am using the GUI provided by Staden, and I was trying
to put the path to phred in the little window in the gui where it says
"phred argument". So I understand now that I don't need to put the path to
phred if phred is already defined in my path, and don't need to use the
"-cd" argument since pregap4 is expecting to find the processed files in the
working directory. Thanks again Malcolm for your help!

Pinar

"Malcolm Cook" <mec at stowers-institute.org> wrote in message
news:4pswa.132$a73.1476 at news.more.net...
> Pinar,
>
> I'm confused by your statement of the problem.
>
> You say you are using pregap4, but your examples look like you are calling
> phred from the UNIX command line, rather than filling in the argument
window
> for the Phred module in pregap4.
>
> In any case, the -cd option does not make sense to use when using phred
with
> pregap4, since the pregap4 phred module writes SCF formatted versions of
> each trace file in the current directory, and rewrites the experiment
files
> to refer to this file, again IN THE WORKING DIRECTORY.
>
> What are you trying to accomplish?  Perhaps you do not need pregap4 for
your
> purposes..
>
> Malcolm
>
>
>
> "Pinar Kondu" <pkondu at attbi.com> wrote in message
> news:Vscwa.575385$OV.547171 at rwcrnsc54...
> > Hi everyone,
> >
> > I am trying to configure Phred in Pregap4. In the argument window for
> Phred
> > module I am putting the following. Program gives me the error message
> > "use -cd with more than one input file".
> > Since I am using it, it seems not to be recognizing my argument. I also
> > tried putting double quotes around, didn't help. Any advice?
> >
> > /usr/local/share/biotools/Phred/phred
> > /var/www/html/seqanal/runphred/abifiles/*.abi
> > -cd  /usr/local/share/seqfiles/processed/phredded
> >
> > (I also tried as:
> > /usr/local/share/biotools/Phred/phred
> > /var/www/html/seqanal/runphred/abifiles
> > -cd  /usr/local/share/seqfiles/processed/phredded
> >
> > AND
> >
> > /usr/local/share/biotools/Phred/phred  .*abi
> > -cd  /usr/local/share/seqfiles/processed/phredded
> > )
> >
> >
> > note:
> > Phred location:
> >  /usr/local/share/biotools/Phred/phred
> >
> > Location of the .abi files that I am adding in the "Files to Process of
> > Pregap4":
> > /var/www/html/seqanal/runphred/abifiles/
> >
> > I am defining a directory for the output so that I can use the "-cd"
> option:
> > /usr/local/share/seqfiles/processed/phredded
> >
> >
> >
> > many thanks,
> > Pinar
> >
> >
> >
> >
>
>




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