questions on ssaha2

[pengchy]

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!