I'm running the genotypes program of Stacks1.46 to generate joinmap output files. This joinmap output file is supposed to be inputted in the JoinMap Software to generate a linkage map. Now, the output from the genotypes program run I got were 4 files: batch_1.genotypes_2.loc batch_1.genotypes_2.txt batch_1.haplotypes_2.tsv and batch_1.markers.tsv.
I tried each one to be uploaded to JoinMap5 but the last 3 on the list created this error:"no "data type" statement in mapmaker (?) file. The first file is the only file recognized by JoinMap5 as "JoinMap Locus Genotype File". But still that first file created this error when uploaded, "no segregation type allowed for this population type at locus 1 (16)"
Any advise how can I proceed given these errors?
