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