104SSAHA2 setup to search for primer binding sites
- Oct 11 4:08 AMHi,
I am trying to setup SSAHA2 to search for primer binding sites in the
human genome. The app we currently have that does this uses BLAST, but
I would like to speed up the search.
The primers will be 15-30bp and I want to allow for up to 2 mismatches
between query and target.
I am planning to read the hashtable in from disk rather store in memory.
Can anyone suggest some appropriate values for -skip and -kmer for
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