Dear all, here are the relevant answers I received concerning my question on amplicon sequencing of microsats. The first paper provides actual data on the next-gen sequencing of microsats. Thank you for all responses. Koen >Hello, I dont have direct experience with this, but i have one idea. You mention "how many X coverage do you need to know the 'correct' allele sizes". This is going to be related to how specific the pcr is, i.e. how much slippage goes on. Well if you run these microsats as 'true' microsats on an abi3730 (or whatever) how much of a stutter peak is there? if these almost no stutter then youd expect the 454 results to give predominantly 2 allele sizes. if theres a lot of stutter then not so much. the other consideration is that if the alleles differ in size by one repeat length (eg alleles sizes 250/252 in a dimer microsat then stutter of one allele can easily give the second allele, but if they differ in several repeats (250/260 in a dimer) then this wont happen Though with 454 it seems like getting microsat data is not the most effective use of your cash (what about RAD tags? eg http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000862)! thats my 2 cents :) >Paper: High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform [Q1] Sarah L. Fordyce1,*, Maria C. Ávila-Arcos1,*, Eszter Rockenbauer2, Claus Børsting2, Rune Frank-Hansen2, Frederik Torp Petersen2, Eske Willerslev1, Anders J. Hansen2, Niels Morling2, and M. Thomas. P. Gilbert1 1 Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark, and 2Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark BioTechniques 51:XXX-XXX (August 2011) doi 10.2144/000113721 Keywords: Short tandem repeat (STR); high-throughput; sequencing; GS FLX Supplementary material for this article is available at www.BioTechniques.com/article/113721. >Paper: Profiling the Dead: Generating Microsatellite Data from Fossil Bones of Extinct Megafauna-Protocols, Problems, and Prospects Morten E. Allentoft1,2*, Charlotte Oskam1, Jayne Houston1, Marie L. Hale2, M. Thomas P. Gilbert3, Morten Rasmussen3, Peter Spencer4, Christopher Jacomb5, Eske Willerslev3, Richard N. Holdaway2,6, Michael Bunce1* 1 Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia, 2 School of Biological Sciences, University of Canterbury, Christchurch, New Zealand, 3 Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark, 4 Wildlife Identification Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia, 5 Southern Pacific Archaeological Research, Department of Anthropology, University of Otago, Dunedin, New Zealand, 6 Palaecol Research Ltd, Christchurch, New Zealand PlosOne 2011 vol6 kdegelas@gmail.com