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Cluster based methods such as multidimensional scaling (MDS) and priniciple component analysis (PCA) are traditionally used in identifying samples with genotypic inconsistencies, however, it is important to identify genotypes with high mendelian inconsistencies prior to any genetic or statistical analysis. In this tutorial, I would like to share how one... [Read More]
Pruning genetic markers based on their physical distance and linkage disequilibrium (LD)
High density markers do not provide any additional information, therefore, can be pruned based on the physical distances between adjacent markers and linkage disequilibrium (LD). In this tutorial, I will show how to prune markers based on their physical position in TASSEL software, and based on LD in PLINK software.... [Read More]
Genome-wide Association Study (GWAS) in TASSEL (GUI)
TASSEL aslo known as Trait Analysis by aSSociation, Evolution and Linkage is a powerful statistical software to conduct association mapping such as General Linear Model (GLM) and Mixed Linear Model (MLM). The GUI (graphical user interface) version of TASSEL is very well built for anyone who does not have a... [Read More]
ANOVA and Tukey test in R software in just few steps!
ANOVA also known as Analysis of Variance is a powerful statistical method to test a hypothesis involving more than two groups (also known as treatments). However, ANOVA is limited in providing a detailed insights between different treatments or groups, and this is where, Tukey (T) test also known as T-test... [Read More]
Marker Assisted Selection using AmpSeq data
This tutorial video is my attempt to introduce the basics of the AmpSeq data analyis in Marker Assisted Selection . For general information on technology behind AmpSeq please read one of my previous blog post on it at this link: https://avikarn.com/2019-04-21-AmpSeq/ [Read More]
Plot Genetic Maps in few steps using MapChart software
MapChart is a free software to plot publishing quality genetic maps as well as QTL data. This software was developed by Roeland E. Voorrips at Wageningen University and can be downloaded at this link . [Read More]
Investigate genetic admixture using STRUCTURE software
Structure Software is a freely available software package that one may use for rigorous investigation of admixed individuals; identification of point of hybridization and migrants; and estimate over all structure of a population using a commonly used genetic markers such as SNPs and SSRs. This software was developed by Pritchard... [Read More]
How to use Multidimensional Scaling (MDS) to quality control your genetic data?
Multidimensional Scaling (MDS) is a powerful statistical method that can be effectively used to elucidate hidden population structure, and more importantly, use it as a quality control tool while working on genetic data. [Read More]
QTL mapping using Composite Interval Mapping (CIM) method in R software
In the Quantitative Trait Locus (QTL) analysis, composite interval mapping (CIM) method estimates the QTL positon with higher accuracy and statistical significance by combining interval mapping with multiple regression. This method also controls background noise resulting from genetic variations in other regions of the genome that affect the detection of... [Read More]
Amplicon Sequencing (AmpSeq): Concept and data analysis
Amplicon Sequencing (AmpSeq) technology combines highly multiplexed PCR sequences of multiple barcoded samples in a single reaction. Amplicons include SNP, haplotypes, SSRs and presence/absence variants. Currently, in a single reaction about 400 amplicons and 3000 samples can be processed simultaneously. In this blog, my goal is to basically introduce the... [Read More]
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