Assigning D84A scaffolds to chromosomes
Working to assign D84A scaffolds to chromosomes. I first took the D84A scaffolds that blasted to both TCO and PA42 and were over 10kb. For each D84A scaffold I asked which PA42 scaffolds it blasted too (match length 5000 or greater), and then asked which chromosomes those scaffolds were anchored too. This was at times slightly complicated as many of the PA42 scaffolds map to more than one chromosome. In some cases D84A scaffolds blasted to multiple PA42 scaffolds that mapped to the same chromosome. This increased my confidence in the assignment. In some cases D84A scaffolds blasted to a single PA42 scaffold that mapped to one chromosome. These were easy to call. But, in some cases D84A scaffolds blasted to one or more PA42 scaffolds that mapped to multiple chromosomes. In those cases I looked at what part of the PA42 scaffold the D84A scaffold mapped too and then which chromosome that part of the PA42 scaffold mapped too. For cases in which the portion the D84A scaffold blasted to on t...