Posted on July 9, 2022

Meuwissen et al 2000 first proposed genomic selection to predict breeding values in animals and plants – the idea was to use DNA markers as predictors in model development to estimate marker effects to predict genomic estimated breeding values. Genomic selection (GS) is becoming a popular technique enabling breeders to... [Read More]

Posted on May 8, 2022

Ideally alleles or haplotype of a single or multiple markers identified post-GWAS or QTL analysis are used to evaluate their effect on a trait of interest. The goal of this tutorial is to visualize the allele effects of a genetic marker on a trait (phenotype) utilizing a R package ggstatsplot... [Read More]

Posted on May 18, 2021

Haploview software is a Java based open source software, developed by Broad institute at MIT for haplotype analysis and LD visualization. I recommend reading more about it at this Link for in-depth information. As per the documentatioin of this software, one can perform wide range of analyses such as LD... [Read More]

Posted on August 30, 2020

Compare imputation accuracies of different imputation methods (Beagle 5.1, LinkImputeR, kNNi, FILLIN) by calculating the percentage of correctly imputed genotypes in TASSEL GUI software. Please find more information on TASSEL software and its documentaton at this Link [Read More]

Posted on August 1, 2020

Multiple Quantitative traits were evaluated with varying heritabilties to study how the inheritance of a trait affect the performance of genomic selection and prediction models. Machine learning algorithms Random Forest and GLMnet: Lasso and Elastic-Net Regularized Generalized Linear Models were deployed to develop Genomic selection models using the publicly available... [Read More]

Posted on July 2, 2020

In this tutorial, negative binomial was used to perform differential gene expression analyis in R using DESeq2, pheatmap and tidyverse packages. The workflow for the RNA-Seq data is: Obatin the FASTQ sequencing files from the sequencing facilty Assess the quality of the sequencing reads Perform genome alignment to identify the... [Read More]

Posted on June 26, 2020

In this tutorial, I used two popular machine learning algorithms: Random Forest and GLMnet for Genomic Prediction of a quantitative trait. There are several machine learning R packages available, however, in this tutorial i used caret package. The objective was to develop two models: Random forest and glmnet using real... [Read More]

Posted on May 26, 2020

R Shiny statistical output visualization app, where a user can upload their own numeric data in .csv or .txt formats, and generate a correlation matrix plots that also contains density plots and printed coefficient of correlation values. Please check it out by uploading your own data below. [Read More]

Posted on August 22, 2019

In this tutorial, I would like to share how one can import SSR (simple sequence repeats) marker data on to TASSEL software, and perfrom analyses such as imputation, General Linear Model and Principle Component Analysis. [Read More]

Posted on August 4, 2019

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]

Posted on July 30, 2019

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]

Posted on July 22, 2019

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]

Posted on July 9, 2019

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]

Posted on June 19, 2019

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]

Posted on May 19, 2019

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]

Posted on May 8, 2019

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]

Posted on May 6, 2019

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]

Posted on April 23, 2019

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]

Posted on April 21, 2019

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]

Posted on April 20, 2019

Genotype-by-Sequencing (GBS) is reduced representation of a genome, which utilizes restriction enzymes (e.g. ApeKI) and NextGen sequencing to identify biallelic markers and presence/absence markers. In this post, my attempt is to consisely present the GBS SNP calling process in 7 steps using the TASSEL GBSv2 pipeline. Pleae note:, Buckler et... [Read More]

Posted on April 17, 2019

Building genetic maps can be challenging and sometimes quite stressful, especially, when dealing with thousands or even millions of markers. In this post, I am hoping to help anyone who would like to get started to build a decent genetic map in an open software Lep-MAP3 , and finally, evaluating... [Read More]

Posted on April 2, 2019

I was interviewed by the Wine Enthusiast Magazine on their special edition on “Wine and Tech”, where i had an opportunity to represent our VitisGen2 project and talk about how computers are being used to “hack” Grapes! [Read More]