[rskr]

thanks @rskr,
I have tried with lots of parameters combinations for both Bowtie and BWA, particularly for the ones reported for illumina reads for aDNA. allowing more mismatches, varying or eliminating seed length, more gaps, etc... Depending on the library, most times I get more mapping reads with bowtie, and with some libraries the difference is not significant. The way I am assessing the quality of the alignment is basically by visualization, that way I can tell if I can see clear SNPs, or DNA damage, or where parameters just were too relaxed and the alignment does not look real. There are no reports for solid data on ancient DNA yet. However there is a paper were different parameters have to be used to get the best alignments for illumina and helicos data on ancient DNA.

The other problem that I have is that for paired data on solid the reads come in the opposite direction and BWA cannot handle them, only bowtie does in theory because I haven't manage to map paired color data yet

Spot checking isn't bad per se.