@isaacovercast Thanks for the fast response! Sorry, I should have been clearer. In addition to getting conventional ddRAD data, I used my ddRAD libraries to make baits and capture very short DNA fragments (ancient DNA, cannot be used for making normal ddRAD libraries), ie enrich these short fragments for my RAD loci. This is to have more overlap between the conventional ddRAD and aDNA sequence reads, and be able to compare the two. For the analysis and for example very basic stats, like calculating capture efficiency, I need to map the aDNA reads to a pseudo-reference to get a ratio of mapped/unmapped reads.