Using TASSEL Getting TASSEL http://www.maizegenetics.net/tassel.

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Presentation transcript:

Using TASSEL Getting TASSEL http://www.maizegenetics.net/tassel

Sequence Hapmap data format Hapmap is a text based file format for storing sequence data. Information on the SNPs as well as germplasm/lines/varities are stored in one file. The first row contains the header labels, and each additional row contains all information associated with a single snp. The first 11 columns described the attributes of the SNP. Genotypes start from The 12th column. Not all positions should be filled for TASSEL to read the data except chrom and pos TASSEL to correctly read Hapmap data, the data must be in order of position within each chromosome/contigs. The file should be TAB delimited format

Numeric Data Used for trait and covariate data such as population structure. Consists of two parts: a header that defines data structure and a body containing the main data. Tabs should be used as delimiters. Trait format starts with <Trait> followed by names of columns Covariate format starts with <Covariate> followed by names of columns. <Trait> Height Yield AGFD_1 56 1000 AGFD_2 67 1300 AGFD_3 66 800 AGFD_4 44 1250 AGFD_5 23 500 AGFD_6 85 1782 AGFD_7 78 1299 AGFD_8 1982 AGFD_9 2011 AGFD_10 89 600

Phenotype data <Trait> Seed_Lg Seed_W Seed_T Seed_100WT Yield_kgha A1 196.1666667 5.551666667 4.85 12.61166667 798.7433333 A2 177 5.748333333 4.38 9.968333333 1019.098333 A3 130.3333333 5.545 4.13 10.11333333 1063.703333 A4 136.6666667 5.403333333 4.593333333 10.16333333 1415.085 A5 134.8333333 4.871666667 4.056666667 10.38166667 942.275 A6 125.1666667 4.791666667 3.805 8.253333333 608.065 A7 169.8333333 5.846666667 4.893333333 11.66333333 990.27 A8 143.8888889 5.694444444 4.793333333 11.21666667 1053.276667 A9 145.3333333 6.083333333 5.015 11.26333333 1066.671667 A10 85.66666667 5.86 4.838333333 9.785 935.015 A11 287.3333333 6.096666667 5.296666667 14.925 1014.375 A12 210.5 5.525 4.623333333 11.02 803.575 A13 175.1666667 5.776666667 4.805 10.995 1248.556667 A14 174.6666667 4.736666667 4.048333333 10.14333333 1165.876667 A15 223.8333333 5.81 4.95 11.75333333 1383.383333 A16 142.8333333 5.518333333 4.625 11.935 1067.893333 A17 152.5 6.005 4.495 11.26166667 830.62 A18 156.6666667 6.038333333 4.741666667 11.38 842.9533333 A19 107.5 5.03 4.22125 9.53125 753.575 A20 99.5 5.885 4.83 10.18833333 964.2983333 A21 199.8333333 5.603333333 4.851666667 12.35666667 1181.418333

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