Shulou(Shulou.com)06/02 Report--

This article will explain in detail how to use TASSEL to do GWAS documentation, the content of the article is of high quality, so the editor will share it with you for reference. I hope you will have a certain understanding of the relevant knowledge after reading this article.

Share an explanatory document I have done, and use the sample data to do GWAS analysis step by step. The details are as follows:

1. Download and install the software

Download address: http://tassel.bitbucket.org/

The 64 system of win is downloaded here, and the screenshot is as follows:

After the installation is successful, open the menu as follows:

two。 Import data

Data download address: http://tassel.bitbucket.org/

The screenshot is as follows:

Open data,load and select Make Best Guess

Select several sample data:

The data after opening is as follows

It includes pedigree data, trait data and genotype data (snp).

3. Processing data

3.1 Clean data

Check mdp_trait

Then select: TransformPhenotype in Data

You can convert and standardize the data. Note that you need to select the data first, and then operate it:

You can also delete the data with missing values, click imput,Numerical impute, and you will generate data with no missing values, which is just a different replacement method for missing values.

3.2 Principal component analysis

Principal component analysis (PCA) is a statistical method, which can transform interrelated variables into independent principal components (PC). The first component contains the most components, and the others decrease in turn. The role of another principal component can be represented by the principal component of the marker. This method saves time than the maximum likelihood method. Because most molecular markers are characters, they need to be converted into numerical values before principal component analysis. Generally, the homozygous marker is replaced by 0, another homozygous marker is replaced by 2, and the heterozygous marker is replaced by 1. PCA requires that variables can not have missing values, so it is necessary to clean the data and remove the missing values in principal component analysis.

To remove the marks whose frequency is less than 0.05, you can select Data, select Site, type 0.05in the box of minimum frequency, then select Remove minor SNP status, and then click Filter to filter. The model is as follows:

Select PCA, then select 5 principal components (default), click OK, and the result will be generated. The model is as follows:

The results are as follows:

3.3 estimation of pedigree by genetic markers

The structural characteristics of the population can be judged by principal component analysis, but if the pedigree information is used, the result will be more accurate. Genealogical information can be generated from genotype data. First, select the genotype data, click Analysis, and select Kinship.

The results are as follows:

3.4. analysis of GLM with general linear model

Next, we use the GLM model to analyze the sample data. Mdp_genotype.hmp.txt is snp data, which contains 3093 markers, 281 maize inbred lines, another file is mdp_population_structure.txt, which contains the population structure of 282 maize inbred lines, and another is mdp_traits.txt, which contains the phenotypic data of 282 maize inbred lines.

First of all, filter the genotype data, remove the frequency less than 0.05, the minimum number is 150, click to filter to generate the filtered genotype data:

Then filter the data and select the character dpoll at flowering stage.

Select the covariable, that is, select the file of the group structure. Here we remove Q3. The data are as follows:

Merge the data, select the three filtered data to merge, and click Data IntersectJoin

The data is merged as follows:

Then the merged data is selected and analyzed with analysis and GLM.

The running results are as follows:

QQ figure:

P-value value:

3.5 Analysis with mixed linear model

The hybrid model needs to add pedigree matrix.

Click run

Results:

Related graphics:

On how to use TASSEL to do GWAS documentation to share here, I hope the above content can be of some help to you, can learn more knowledge. If you think the article is good, you can share it for more people to see.

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.