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[Bio-software] Questions about megablast

JI QI jxq11 at psu.edu
Tue Mar 28 10:24:41 EST 2006

Dear Dr. Madden,

Could you help me with several problems of megablast?
I used megablast these days and find 3 problems when outputing
blast-like results.

1. Some reads were missed from the results.
2. Some reads appeared several times in the results.
3. Some reads got some hits but their complementary sequences
   do not hit anyting.

The megablast works well when using small input datasets, however,
it has some problem when using large dataset (about 300,000 reads).
Here is my call for megablast:
"megablast -V F -H 4 -F F -D 2 -v 0 -M 500000000 -d"
Is there anyting wrong with the command?

Your reply will be highly appreciated.


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