Does anyone know why reads from a paired end solexa run that are aligned using ./maq map are mixed upper and lower case letters in the resulting.txt alignment file? eg:
GggTTAgGGTTAGGgTTaGGGGTTAGGGGTTAGGGgTTAGGGTTg
Cheers
L
GggTTAgGGTTAGGgTTaGGGGTTAGGGGTTAGGGgTTAGGGTTg
Cheers
L