Hi,
I've tried reading the manual to answer this one, but it's not behaving how i'd expect . I'm trying to map 454 reads to a reference with a very high stringency (so i don't get miss-mapping to repeat regions).
From the manual it seems the -mi (Flag to set the minimum overlap identity parameter) and -ais (Flag to set the alignment identity score parameter) flags are what i need to use. But though the flags seem to change the mapping (as measured by the number of unmapped reads) i don't seem able to input a value for the desired %ID cut off, e.g. "-mi 99" and "-mi 100" give identical results.
Any tips would be much appreciated.
Cheers,
Kirstin
I've tried reading the manual to answer this one, but it's not behaving how i'd expect . I'm trying to map 454 reads to a reference with a very high stringency (so i don't get miss-mapping to repeat regions).
From the manual it seems the -mi (Flag to set the minimum overlap identity parameter) and -ais (Flag to set the alignment identity score parameter) flags are what i need to use. But though the flags seem to change the mapping (as measured by the number of unmapped reads) i don't seem able to input a value for the desired %ID cut off, e.g. "-mi 99" and "-mi 100" give identical results.
Any tips would be much appreciated.
Cheers,
Kirstin
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