[brentp]

bisol,
are you encountering a specific problem or do you have a better solution?
perhaps I can help and we can improve the available tool-set for mapping bisulfite-treated, colorspace reads.

You are now suggesting that all unmapped reads should instead be aligned with
SOCS-B, which - even though it is a good tool - is incredibly slow for complex
genomes and many reads.

This is exactly why I think mapping as many reads as possible with a fast solution
is a reasonable compromise. I have not suggested otherwise.