I have RNA-seq data of several varieties from the same plant species. I also have a genome from, let's say, ancestor of that species, which I am going to use as a reference. I am interested in studying SNPs (Single Nucleotide Polimorphisms). Which aligner do you suggest me to use in order to map my RNA-seq data to the reference genome? I am thinking to go for TopHat.
Also, could you suggest some pipeline to do this kind of analyses?
P.S. there is a problem of homoeologous genomes in my plant species