SSR data conversion for new version TASSEL 5

[RAFIQ AHMAD SHAH]

Respected group members

 I have SSR data and want to convert it into SNP data for analyzing it newer version of TASSEL. How could I do this. Kindly help. The record of SSR excel sheet is attached.

[Peter Bradbury]

See the FAQ at the bottom of the File/Open page in the User Manual (https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/Load/Load):

FAQ

Can I import non-nucleotide data, such as SSR data, into TASSEL?

Yes. To import non-nucleotide data into TASSEL 5.x, alleles should be recoded using the nucleotide symbols (A,C,G,T,+,-) in diploid hapmap format. Doing so provides a way to import chromosome and position for each site. If any site has more than 6 alleles, only the five most common alleles should be coded separately and the remaining alleles should be pooled together as ‘-‘. Alternatively code each allele as a separate site with each allele in turn coded as A and any other allele coded as C. Numeric values for the data can be imported into TASSEL 4.x using the polymorphism format described in the TASSEL 3 User Guide. Warning: it is the users responsibility to make sure that any subsequent analysis is appropriate for their data. Some TASSEL methods, such as LD and Association Analysis, are best suited for bi-allelic data. For example, LD analysis pools only minor alleles into a single class, thus forcing all data to be bi-allelic prior to analysis.