I am processing Illumina reads from many lanes. We are mainly interested to study SNPs, recombination etc in chromosomes (2L, 2R, 3L, 3R, 4 and X). I have a basic question regarding "mapping of reads to the Drosophila genome": Do I need to include chromosomes Het, U and Extra's for mapping or exclude them and map to the rest of the genome. How does this affect? I need your thaughts in support or against.