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Import from CEQ8000

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Weig
2012-01-18
2013-04-15
  • Weig
    Weig
    2012-01-18

    Hello,

    I have separated fragments on a CEQ8000 capillary electrophoresis machine (Beckman-Coulter). Since the fragments are quite long (up to 1200 bp), the Beckman software had some problems to size the fragments correctly. I used a combination of the 60-600 bps Beckman standard together with a 600-1200 Bioventures standard (recommended by Backman). I have a new standard definded in the Genographer cfg file an tried to import scf files exported by the Beckman software. But the import manager will not accept these files! I'm not sure what exactly CEQ trace files are. The raw data files (*.cqs) are not accepted, and I also tried *.crv files exported from the beckman fragmen module (no import possible). The crv files are however only available if a previous (sucessful) analyses of the raw data files has been done. Since this does not work well, I'm wondering whether I should use it.

    Therefore, I would like to use the raw data from SCF files. Is there any suggestion how to import these files or hwo to check whether these files are in the correct format for import.

    Thanks for any suggestion!
    Alfons

     
  • Travis Banks
    Travis Banks
    2012-01-18

    Hi Alfons,

    Email a copy of the SCF to my gmail account.  I'll see if I can figure out what's going wrong.  I didn't have access to a Beckman machine or data when programming this version of Genographer so it doesn't surprise me it doesn't work quite right.

    Travis

     
  • carlo
    carlo
    2012-02-02

    Hi Travis,
    I am facing similar problems: I  am trying to import CEQ 8000 exported (.txt) files with the latest version of Genographer 2.1.4 installed on a Window 7 machine (2GB of memory available).
    The import file window allows me to select the .txt file, to specify the CEQ trace type, to select 'don't size' (I would like to analyze AFLP fragments and be able to align manually each lanes) but after hitting the 'import' button the software is not importing anything!
    What am I doing wrong?
    The very same .txt file is imported by a older version of Genographer 1.6.0 but I don't know where to find Istallation files for such older version, also I don't know if it will run on Win7 OS, and lastly it looks like not as user friendly as the latest version 2.1!
    Any suggestion on how let the latest version of genographer import CEQ 8000 files for AFLP analysis will be really apreciated!
    Thanks
    Carlo

     
  • Travis Banks
    Travis Banks
    2012-02-03

    Hi Carlo,

    When I rewrote Genographer I didn't have access to a CEQ 8000 file.  If you send me the raw file or text file I'll see if I can see why it's not loading the data.  If it worked on the old Genographer I'm sure I can get it to work with version 2.1

    Travis

     
  • carlo
    carlo
    2012-02-06

    Hi Travis,
    I've sent a personal message to you via this forum: it is a txt file exported from a CEQ8000.
    Have you got it?
    if not, please let me know your gmail account, it seems I can't find it.
    thank you
    Carlo

     
  • Travis Banks
    Travis Banks
    2012-02-06

    Hi Carlo,

    Yes I received the email.  I'll take a look at the CEQ8000 data over the next few days.  Can you tell me a bit about the run;  how many samples, number of fragments, do you expect to see polymorphism, etc?

    Travis

     
  • carlo
    carlo
    2012-02-06

    Hi Travis,
    that's a file containing data from a single sample, one capillary run.
    D1 is the fluorophore for the Molecular Size Standard
    D2 is not used in this run
    D3 and D4 are used each one for a different primers combination (therefore you'll see a different fragment profile)
    I have sent you only one file since importing was the issue but if you need I'll send you another one.
    looking forward for news from you, thank you
    Carlo

     
  • Travis Banks
    Travis Banks
    2012-03-24

    Hi All,

    I've worked out a fix for the problem with CEQ files.  I'll release it in version 2.1.5.  I have to pick up some software to create the windows and mac release before I put it on the web.  Contact me if you want the fix by email.

    Travis