Microsatellite Analysis in Geneious Prime

This microsatellite analysis series shows how to fit ladders, set loci, and bin alleles using the Microsatellite plugin in Geneious Prime. Correct missing or incorrect peaks, including stutter and pull-up artifacts, before binning, then export the allele table as CSV or review allele size distributions. The three videos of 2 to 4 minutes each, must be watched in order.

Course Content

1. Fitting Ladders for Microsatellite Analysis

Install the Microsatellite plugin, then check that ladders are called correctly using the Traces and Ladder tabs. Fix diverging, missing, or incorrect peaks and correct over-trimming, then scale the X axis to base pairs before setting loci.
LENGTH 4 minutes

2. Setting the Loci for Microsatellite Analysis

Set the expected number of peaks, repeat unit, and range for each locus in the Locus Information window, then save the loci as a named file. Review each trace for stutter, slippage, or pull-up artifacts, correcting or adding peaks as needed.
LENGTH 2 minutes

3. Binning for Microsatellites

Predict bins for each dye after setting loci, then review the Alleles Table and fix any unbinned peaks by extending the bin range. Export the allele table as CSV, or check the Allele Size Distribution graph for each dye.
LENGTH 2 minutes

Recommended Resources

Plugin - Microsatellites Plugin

Download the Microsatellite plugin for Geneious Prime.

Microsatellites FAQS

Common questions on using microsatellite analysis in Geneious Prime.

Manual for Microsatellite Analysis

Guide to using the microsatellite analysis tools in Geneious Prime.

Getting Started with Microsatellites

Learn to use the Microsatellite Plugin to analyze traces from ABI fragment analysis machines.

More Geneious Academy

TUTORIALHow to Analyze Microsatellite Traces in Geneious Prime
Fit a ladder, call peaks, bin alleles and produce a genotype table with the Microsatellite plugin.
Read Tutorial
VIDEO SERIESSanger Sequence Analysis in Geneious Prime
Trim and map Sanger chromatograms to a reference, then call SNPs, review their effect on protein coding, and export your variants.
Watch Series
TUTORIALHow to Assemble Chromatograms in Geneious Prime
Assemble bidirectional Sanger reads from blue tit mitochondrial DNA and extract high-quality consensus sequences.
Read Tutorial
VIDEO SERIESDe Novo Assembly in Geneious Prime
Learn to assemble NGS reads without a reference genome, covering sensitivity settings, read normalization, and circular genome assembly in Geneious Prime.
Watch Series
Get started with Geneious today
Try Geneious FreePricing