changing %ID for runMapping on GDS software package version 2.3.1

[Kirstin]

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

[vamosia]

You'll mostly likely need to play around with the parameters to see what best work for you data, but in my case the 90% identity and 80% query coverage (-mi 90% -ml 80%) gives the best results for my human mapping.