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Old 07-20-2017, 07:49 AM   #1
tugecko
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Location: Philadelphia

Join Date: Jun 2017
Posts: 3
Default Optimal coverage for sequencing microsatellites with Illumina

My lab is planning a phylogeography study on several different groups of lizards using microsatellites. We are interested in pooling the microsatellite amplicons for all of our individuals and then sequencing that library on an Illumina HiSeq 2500 machine (perhaps not the optimal machine for this project, but the one we have access to).

Right now, we are trying to figure out the logistics of our protocol, and one thing that we are stuck on is how much coverage we want per microsatellite locus per individual (which determines how many we could pool, etc.). I imagine that one would want more coverage than for a RAD protocol, since there are more potential variants one could be detecting, but I am really not sure. We haven't developed our microsatellites yet, so we don't know how much allelic variation we will be dealing with.

Has anyone else done a similar protocol with microsatellites? Does anyone have any advice? The few papers I found had wildly different amount of coverage (one had ~ 13x, which they determined was not enough, and the other 2000x, which seems excessive)

Just starting out, any thoughts would be appreciated!
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