maq map -n in colorspace

[Mr Mutundes]

Hi,

I have been investigating the use of MAQ 0.7.1 for aligning SOLiD reads to a reference and calling SNPs. I am wondering about the behaviour of the -n option which sets maximum mismatches allowed when using maq's map command. MAQ allows only values of 1,2 or 3 for this option. Since in colorspace a SNP is comprised of two adjacent color changes does this mean that reads with more than one SNP cannot be aligned with maq map?

Thanks for any help.

Mr M

[Chipper]

Not sure about MAQ, but bwa works well with CS. You can set it to allow 2 mismatches in the first (good part) of the read and several in the last part and still get good speed (and more unique alignments than mapreads). But my impression after some extensive testing is that BFAST is the best option since it is able to place more low-quality reads uniquely as well as using the first color. Have not yet tested if the low-quality alignments are correct though...

[Mr Mutundes]

Thanks Chipper