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  • questions on ssaha2

    Hi all,

    I have several questions on ssaha2 after reading through ssaha2-manual.

    1. how to randomly report one best hit if there are many hits?
    What's the meaning of bval=2 of the paramter -best?

    2. Is the parameter "-solexa" and "-rtype solexa" exactly same?

    3. Can the output file in ".gz" format, which will reduce the storage?

    4. what's the parameter "-array" stand for? How can I deduce what large this parameter should be according to my data?

    5. what's the parameter -skip will influence?
    In the manual:
    -skip stepsiz Sets the number of nucleotide letters between the starting letter
    of successive words. I.e. With the option -skip 1 every word is hashed,
    with -skip 2 every second word, with -skip 3 very third etc.
    according to my understand, this parameter will influence the reported segment. If the terminal n bp (n < skip) in the read is not covered by one kmer exactly, this n bp will not be reported. The smaller skip will slow the speed. Is there a evaluation of the mapping probability influenced by different skip size?


    Any reply or suggestions will be highly appreciated!
    Last edited by pengchy; 09-25-2011, 02:50 AM.

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