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change sequences' format: from ab1 to scf

2006-12-11
2013-04-18
  • Hello,
    I'm looking for a possibility to change the format of a group of sequencing files from .ab1 to .scf. I found how to do it in Staden (Trev) but only one by one. It takes time and I've got an awful lot of files. Waht I need is to change the format of several files (e.g. all in a selected folder) at once. Can anybody help, please? Thanks.
    kasiasz

     
    • asjo
      asjo
      2006-12-11

      Does convert_trace do what you want?

      Something along the lines of:

      convert_trace -out_format scf < test.ab1 > test.scf

      ?

       
    • deKesi
      deKesi
      2006-12-11

      Hello,

      What about creating a file of filenames with the files you want to convert and let pregap work for you?
      Just disable all modules except of "trace format conversion" and select ".scf" for output format.

      For further instructions have a look at the manual.

      Best regards,

      deKesi

       
    • PreGap works great (took me some time as I had never used Staden before but it seems to be working now). Thanks a lot for the advice!
      kasiasz