Post date: Jan 27, 2017 4:8:5 PM
I have been playing some with orientating scaffolds based on the recombination rates. I haven't completed orientations or mapping based on the green genome yet (variant calling now), but I have tried orientating and ordering on LG8 based on the brown versus green parent aligned to the brown genome. The results look promising, but I will want to do more once I have recombination rates based on the green parent aligned to the green genome. Anyway, here are plots of the four key scaffolds, 128, 702.1 and the ones on each side of these (brown, green). I have a set of four images based on green vs. brown recombination. Note first that the overall direction of the map flips between the two, but this is arbitray (just think of things going from one end to the other). The plots are position (in cM) versus position in bp and scaffolds are ordered based on the ordering for that parent. First note that the order of 128 and 702.1 with respect to the flanking scaffolds switches, this is cool. Also, their orientation switches, which is just what you would expect for an inversion. For most scaffolds orientation is pretty clear (positive or negative correlation between physical position and cM). But, with 702.1 this is far weaker (and actually non-significant) than the others. This would make sense if there is little or no recombination within 702.1. I will generate another round of results when I have the proper green on green. That will be a bit trickier as I will have to cross-reference with the comparative alignment and do about of mental flipping things back and forth, but I am pretty optimistic we will have a clear answer in terms of comparative order and orientation for all or most of the LG.
Code here (compOrient.R, in /uufs/chpc.utah.edu/common/home/u6000989/data/timema/timema_mappingfams/mapdata/lm2map:
## read LG and SNP information
snps<-read.table("combinedSnpList.txt",header=F)
map<-read.table("order2_LGbrwn4tcr.txt",header=F)
scafs<-snps[map[,1],1]
pos<-snps[map[,1],2]
cms<-map[,3]
pdf("brownOrientation.pdf",width=8,height=8)
par(mfrow=c(2,2))
plot(cms[scafs==2963],pos[scafs==2963],xlab="position (cM)",ylab="position (kb)",cex.lab=1.2)
r<-cor(cms[scafs==2963],pos[scafs==2963])
title(main=paste("scaffold 2963, cor = ",round(r,3)),adj=0)
abline(v=median(cms[scafs==2963]),lty=2)
plot(cms[scafs==702.1],pos[scafs==702.1],xlab="position (cM)",ylab="position (kb)",cex.lab=1.2)
r<-cor(cms[scafs==702.1],pos[scafs==702.1])
title(main=paste("scaffold 702.1, cor = ",round(r,3)),adj=0)
abline(v=median(cms[scafs==702.1]),lty=2)
plot(cms[scafs==128][-c(1,29)],pos[scafs==128][-c(1,29)],xlab="position (cM)",ylab="position (kb)",cex.lab=1.2)
r<-cor(cms[scafs==128][-c(1,29)],pos[scafs==128][-c(1,29)])
title(main=paste("scaffold 128, cor = ",round(r,3)),adj=0)
abline(v=median(cms[scafs==128]),lty=2)
plot(cms[scafs==1845][-19],pos[scafs==1845][-19],xlab="position (cM)",ylab="position (kb)",cex.lab=1.2)
r<-cor(cms[scafs==1845][-19],pos[scafs==1845][-19])
title(main=paste("scaffold 1845, cor = ",round(r,3)),adj=0)
abline(v=median(cms[scafs==1845]),lty=2)
dev.off()
map<-read.table("order2_LGgrn4tcr.txt",header=F)
scafs<-snps[map[,1],1]
pos<-snps[map[,1],2]
cms<-map[,2]
pdf("greenOrientation.pdf",width=8,height=8)
par(mfrow=c(2,2))
plot(cms[scafs==2963],pos[scafs==2963],xlab="position (cM)",ylab="position (kb)",cex.lab=1.2)
r<-cor(cms[scafs==2963],pos[scafs==2963])
title(main=paste("scaffold 2963, cor = ",round(r,3)),adj=0)
abline(v=median(cms[scafs==2963]),lty=2)
plot(cms[scafs==128],pos[scafs==128],xlab="position (cM)",ylab="position (kb)",cex.lab=1.2)
r<-cor(cms[scafs==128],pos[scafs==128])
title(main=paste("scaffold 128, cor = ",round(r,3)),adj=0)
abline(v=median(cms[scafs==128]),lty=2)
plot(cms[scafs==702.1],pos[scafs==702.1],xlab="position (cM)",ylab="position (kb)",cex.lab=1.2)
r<-cor(cms[scafs==702.1],pos[scafs==702.1])
title(main=paste("scaffold 702.1, cor = ",round(r,3)),adj=0)
abline(v=median(cms[scafs==702.1]),lty=2)
plot(cms[scafs==1845],pos[scafs==1845],xlab="position (cM)",ylab="position (kb)",cex.lab=1.2)
r<-cor(cms[scafs==1845],pos[scafs==1845])
title(main=paste("scaffold 1845, cor = ",round(r,3)),adj=0)
abline(v=median(cms[scafs==1845]),lty=2)
dev.off()