coding SSR as SNP in tassel 5.0-help

[Senthilkumar Shanmugavel]

Hi every one.

    im trying to perform structured association analysis. we had used SSR markers on sugarcane which is a polyploid , also genome information is not known and the markers are scored as "1" for presence and "0" for absence. in TASSEL 5.0 user guide says to change SSR as SNP like wise to change the first major allele to A and next to C and so on. so in my case "1" will be coded as A and next should "0" should be coded as C or should be coded as "-". can some one help me regarding this

thanks

[Peter Bradbury]

It does not matter. You are just substituting one symbol for another. A, C, G, T, +, and - are symbols that Tassel recognizes. Substitute one of those for 1 and a different one for 0.

Peter

[Senthilkumar Shanmugavel]

Hi peter

   i had made the changes as told by by you, now i'm getting an error that "position should be an integer" i had assigned "NA" to all the data we dont have as chromosome number, position ,strand,assembly# ,center, protLSID,assayLSID,panel, QCcode is that right ?. or it some dummy numbers can be added ?

thanks

[Senthilkumar Shanmugavel]

Thank you Peter 

 

On Monday, April 25, 2016 at 6:27:25 PM UTC+5:30, Peter Bradbury wrote:

[Peter Bradbury]

Chromosome and position are required. Chromosome can be anything (including NA or 0). Position must be an integer. You can just number them sequentially, 1 to N if you do not have any estimate of position.

Peter

[K K Vinod]

Tassel identify data only in certain format. Its better to use HapMap format for SSR data. Please check the Tutorial data to know more bout this format.

Vinod