Entering edit mode
3.7 years ago
safiq713
▴
10
Dear all
I want to keep some loci, only those loci has 4 SNPS (specific number of SNPS). I want to make skyline plot from ddRAD data. Do you have any idea how can go forward
Thanks a lot for your help
may be you can create sliding windows and count SNPs within them and keep the ones that has more than 'n' SNPs. and then merge overlapping windows post-hoc to have a consensus loci. This can be achieved by bedtools and a bit of scripting. I am not aware of any tools that does this.