Automatic genomic alignment

  • Nobody/Anonymous

    Im sitting with several thousands abi-files/chromatograms that need be located onto the mouse genome.
    I would be very greatful to any who can tell me a way to speed up the process (i have the feeling that the Staden package can help me, at least partially - it must be a common 'problem' to many - but im rather newbee in the bioinformatics).
    I need to do the following:
    1) remove some vector sequence
    2) identify the insert orientation (from the sequence of step 1))
    3) align to the murine genome
    4) retrieve results

    In advance: thanks

    Mads Rasmussen

    • James Bonfield

      James Bonfield - 2007-02-02

      Removal of vector can be achieved using Pregap4's vector_clip module or via cross_match. Crossmatch is a blunt instrument, but simpler to use.

      For mapping against the genome, to be honest I'd say something like ssaha2, blast, blat, etc (a quick google should help find them) is a quicker route, or cross_match again.



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