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  • *.asc files from capillary sequencing

    I've got a number of *.asc files from some capillary seqeuencing, in which the README proclaims the following format. If anyone has experience with this format, I'd really like to understand how the fragment size relates to the number of nucleotides in the allele. Any input or speculations welcome! I have not been able to find information on this file format anywhere...

    AFM240zf4 <--------probe name field at line 1
    (AC)n <--------probe description field
    D20S181 <--------D-number from GDB
    Z23780 <--------gene symbol (or Z-number from Genbank)
    4 <--------number of fragments
    4 <--------number of alleles (up to 36 alleles)
    20 <--------chromosome (1 to 22, 23 is X, 24 is Y, 25 is pseudoautosome)
    q <--------arm of this chromosome (p, q, b for both or c for centromere)
    0.000000E+00 <--------cytogenetic location *
    0.000000E+00 <--------cytogenetic location **
    0.000000E+00 <--------gene location
    5.555556e-01 <--------observed heterozygote frequency
    102193 <--------last update mmddyy
    p <--------status p (published) u (unpublished), all data considered published
    0 <--------Reliability
    42 0 0 0 <--------CEPH collaborator code number
    Genotyped <--------interpretation
    1.600000E-01 1.560000E-01 1.640000E-01 1.660000E-01 <-- size of fragments
    1 2 3 4 <-- correspondence alleles/fragment
    3.888889e-01 2.500000e-01 3.611111e-01 0.000000e+00 <-- allelic frequencies
    1326 8067 1 0 0 1
    1326 8065 2 0 0 2
    Last edited by oiiio; 01-29-2014, 01:19 PM.

  • #2
    cross posted on biostar: http://www.biostars.org/p/91988/

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    • #3
      Can you elaborate on why you think these are capillary sequence files?

      Following may be totally out in the left field but I am wondering if these are files from GDB (human genome database) which is a now extinct database that was started back in beginning of human genome project at Johns Hopkins (late 1980s). The D-numbers and the date (1993) all seem to point to GDB.

      See page 8 from this PDF: http://web.ornl.gov/sci/techresource...fs/Vol4No2.pdf
      Last edited by GenoMax; 01-29-2014, 05:38 PM.

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