TASSEL关联分析软件用户指南

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"TASSEL用户指南" TASSEL（Trait Analysis by aSSociation, Evolution and Linkage）是一款功能强大的关联分析工具，由 Buckler Lab at Cornell University 开发。该工具旨在帮助研究人员对植物 Trait 进行关联分析，探索植物性状之间的相关性。 **TASSEL 的主要功能** 1. 关联分析：TASSEL 可以对植物的Trait 进行关联分析，探索不同Trait 之间的相关性。 2. 演化分析：TASSEL 可以对植物的进化关系进行分析，探索不同植物之间的演化关系。 3. 链接分析：TASSEL 可以对植物的Trait 之间的链接关系进行分析，探索不同Trait 之间的交互作用。 **TASSEL 的应用领域** 1. 植物育种：TASSEL 可以用于植物育种中，探索植物性状之间的相关性，帮助育种工作者选择更好的育种策略。 2. 基因组学：TASSEL 可以用于基因组学中，探索基因之间的相关性，帮助研究人员更好地理解基因的功能。 3. 系统生物学：TASSEL 可以用于系统生物学中，探索生物系统中的相关性，帮助研究人员更好地理解生物系统的运作机理。 **TASSEL 的使用指南** 1. 数据导入：用户可以将数据导入到 TASSEL 中，进行关联分析、演化分析和链路分析。 2. 参数设置：用户可以根据需要设置参数，例如选择分析方法、设置阈值等。 3. 结果解释：TASSEL 将提供分析结果，用户可以根据结果进行解释和应用。 **TASSEL 团队** 1. 项目领导：Ed Buckler 2. 数据导入：Terry Casstevens 3. 统计分析：Peter Bradbury 4. 贡献者：Yogesh Ramdoss, Michael E. Oak 等 **TASSEL 用户群** TASSEL 用户群是一个在线社区，用户可以在这里与其他用户交流经验，分享知识和资源。 **TASSEL 的优点** 1. 强大的关联分析功能 2. 广泛的应用领域 3. 易于使用的界面 4. 活跃的用户群 **TASSEL 的注意事项** 1. TASSEL 的结果可能不太可靠，用户需要对结果进行验证。 2. TASSEL 需要与其他软件结合使用，以确保结果的可靠性。 TASSEL 是一个功能强大且广泛应用的关联分析工具，对植物育种、基因组学和系统生物学等领域的研究人员非常有价值。

2.2.1 BLOB

A Binary Large Object (BLOB) is a collection of binary data stored as a single entity. In TASSEL,

BLOBs are used to compress large data sets into more manageable sizes. For sequence data, three types of

BLOBs are used: SNP value BLOB, position BLOB and SNP ID BLOB. The three BLOBs are used to

store individual SNP values, SNP position within the genome and the SNP identifiers respectively.

A BLOB is composed of two components, a header and a body. The header for each BLOB is 1024 bytes

long, while the length of the body depends on the type of BLOB and on the amount of data being stored.

For a more detailed description on the structure and information contained within the header and body,

refer to the GDPDM BLOB Specifications.

(http://www.maizegenetics.net/gdpdm/docs/20100526/GDPDMBlobSpecification_20100526.pdf)

2.2.2 Hapmap

Hapmap is a text based file format for storing sequence data. All the information for a series of SNPs as

well as the germplasm lines is stored in one file. The first row contains the header labels, and each

additional row contains all the information associated with a single SNP. The first 11 columns describe

attributes of the SNP, while the following columns describe the SNP value for a single germplasm line.

The first 12 columns of the first row should look like this, where “Line 1” is the beginning of germplasm

line names.

rs#

alleles

chrom

pos

strand

assembly#

center

protLSID

assayLSID

panelLSID

QCcode

Line 1

While all 11 header columns are required, not all 11 of the columns need to be filled in for TASSEL to

correctly interpret the data. The only required fields are “chrom”, Chromosome name, and “pos”,

Position.

For TASSEL to correctly read Hapmap data, the data must be in order of chromosome and position within

each chromosome, and the file should be TAB delimited. If some of the data is missing the correct

number of TABs must still be present, so that TASSEL can properly assign data to columns.

2.2.3 Plink

Plink is a whole genome association analysis toolset, which comes with its own text based data format.

The data is stored in a set of two files, a .map file and a .ped file.

The .ped file contains all the SNP values and has six mandatory header columns for Family ID, Individual

ID, Paternal ID, Maternal ID, Sex and Phenotype. TASSEL only requires that the Individual ID field be

filled in. Each row of the .ped file describes a single germplasm line. Notice in Plink, an unknown

character is represented with a '0'. However in TASSEL an unknown character is represented with a 'N',

and '0' is used to represent heterozygous indel. TASSEL will automatically convert between the '0' and the

'N'. Any exported Plink files will represent the heterozygous indel with a '+' (insertion) and a '-' (deletion).

The .map file describes all the SNPs in the associated .ped file, where each row provides information on

one SNP. The .map file must contain exactly four columns: Chromosome, rs#, Genetic distance and

Position. TASSEL does not require the Genetic distance field to be filled in.

Both files should be TAB delimited.

For a more detailed description on the data format, please visit the Plink basic usage and data formats

webpage: (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml).

2.2.4 Flapjack

Flapjack is a software tool for graphical genotyping and haplotype visualization. The program is capable

of outputting data in its own text based data format. Like Plink, the data is stored in a set of two files, a

.map file and a .geno genotype file.

The genotype file contains all the SNP values. Each column in the first row contains a SNP ID, except for

the first column, which is blank. The first column of the following rows contains the germplasm line

names. TASSEL requires that all fields be filled out in order for data to be read correctly.

The .map file describes all the SNPs associated with the genotype file. Each row describes a single SNP.

There are three columns in the .map file for Flapjack, SNP ID, Chromosome and Position, all of which

are required for TASSEL to run correctly.

Both files should be TAB delimited.

For a more detailed description on the Flapjack data file format, please visit the Flapjack data import

website: (http://bioinf.scri.ac.uk/flapjack/help/gui.dialog.DataImportDialog.shtml).

2.2.5 Polymorphism

A general format that accepts almost any type of marker data can also be used. Any alphanumeric

character is allowed. Diploid data can be represented by separating alleles with a colon (“:”), for example

A:A, A:B, or B:B. All loci in a file must have the same ploidy level. The first line starts with the symbol

<Marker> followed by the marker names. Subsequent lines must start with the name of the individual or

taxon genotyped followed by the marker scores in the same order as the header. Comments can be

inserted at the beginning of the file as long as any comment lines begin with the symbol “#”. Columns are

TAB delimited. Numeric values are allowed but, by default, will be treated as classification variables not

as covariates in analyses.

Example 1:

<Marker> m1 m2 m3 m4 m5

33-16 A B B A A

38-11 A A B A A

4226 A B B A B

In some cases, a user may wish to have marker values treated as numerical covariates. If the first line of

the file is “<Numeric>”, then the data will be imported as numeric data but used as marker data in GLM

and MLM.

Example 2:

<Marker> m1 m2 m3 m4 m5

33-16 0 1 1 0 0

38-11 0 0 1 0.3 0

4226 0 1 1 0.5 0

Note to TASSEL 2.1 users: The polymorphism format specified in TASSEL v2.1 is still supported to

provide backward compatibility.

2.2.6 Phylip

The Phylip format used by TASSEL version 2.1 will continue to be supported. Details on Phylip format

are described at the following website: http://evolution.genetics.washington.edu/phylip/doc/sequence.html

2.2.7 Numerical data

This type of format is used for trait and covariate data such as population structure. Similar to sequence

alignment genotype data, numerical data also consists of two parts: a header that defines data structure

and a body containing the main data. Tabs should be used as delimiters. However, any white space

character such as blank will be treated as a delimiter as well. As a result, embedded blanks in names will

cause data to be imported incorrectly. We suggest representing missing values using “NA”, or “NaN”.

However, any text value (e.g. “?”) will be interpreted as missing data. There are several formats for

numerical data to fit the requirement for modeling. Trait data (dependent variables) can be imported by

starting the first line with “<Trait>” and following that with the trait names. Additional classifiers may

also be included in subsequent header rows by starting the row with “<Header name=xxx>” followed by a

name for each column of data. For instance, to define environments, start the second header row with

“<Header name=env>”.

Comment lines may be inserted at the beginning of the file as long as each comment line begins with the

character “#”.

2.2.7.1 Trait format

This format does not require users to provide information on number of rows and columns. The file stats

with key word <Trait> followed by names of columns. The column for line should not be labeled.

Example 1, simple list of trait values:

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