Dear Dr. Madden,
Could you help me with several problems of megablast?
I used megablast these days and find 3 problems when outputing
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.