I have mapped RAD-PE reads to a reference genome (that consists only of scaffolds without the assignment of scaffolds to any chromosome) called SNPs and calculated FST values between populations. I now want to create manhattan plots of FST values with scaffolds arranged into chromosomes. However as the reference genome for my species consists only of unarranged scaffolds I have used satsuma synteny to assign and order scaffolds to chromosomes based on the fully assembled genome Zebra Finch genome. I now have a spreadsheet that has the columns below and with scaffolds listed in order.
Headings: - chromosome that scaffold is assign to - scaffold - mean location of scaffold - scaffold orientation
My question is how do I now use this output when plotting FST? Does anyone have experience of using satsuma synteny?