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Microsatellite Parameterized Analysis Tools
MicroSPAT is a collection of tools for semi-automated analysis of raw capillary electrophoresis (CE) data output by the ABI 3730, and has been designed specifically for working with multi-allelic samples. MicroSPAT was developed in the Greenhouse Lab with the goal of improving reproducibility and consistency of microsatellite analysis between analysts.
MicroSPAT integrates several features to improve reliability of analysis including a plate view for quality checking of the experiment, automated ladder identification, automated bin generation using a clustering algorithm, automated identification and filtering of stutter peaks or artifact, estimation of amplification bias due to fragment length differences, and automated genotyping of samples using parameterized settings for reproducibility, with the option of manual curation. If you're using MicroSPAT, please Star the repo so that I know it is of use to people.
The latest release of MicroSPAT can be found here To first get started, the user must configure a number of settings before loading any raw data.
- The genetic loci to be analyzed must be added. Instructions on how to do this can be found here
- Then the loci to be analyzed must be added to a
Locus Set
. This is discussed here - Next, the user must generate the settings for the ladder to be used for analysis. Details about this may be found here
- After specifying the ladder, the user may start to upload their data. Instructions regarding this process are found here
- Finally, with data loaded and samples generated, the user may begin their analysis. First the user must generate a Bin Estimator, details may be found here.
- With a Bin Estimator created, the user may also create an Artifact Estimator as outlined here, or simply begin their analysis as outlined here.