Post date: Mar 04, 2014 10:34:48 PM
I created new linkage groups based on the new mapping family data. The scripts and analysis are in projects/timema_lgs/v2 (the old stuff is in v1). The key R script is makelg. The new genome includes 1413 scaffolds vs. 1312 before. Whether or not scaffolds were on the same LG was highly correlated between the two drafts, r = 0.8 (in other words, scaffolds that were on the same LG before are mostly on the same one now too). So, all in all, the genome didn't change that much, although the size of the genome in units of recombination shrank to about 50% of what it was (i.e. we now have better estimates of recombination, although the total recombination size is still too big). I might still play with this a bit more before assembling the whole genome data, but we are certainly making progress. In particular I could include smaller scaffolds or assign recombination rates other than 0.5 to scaffold pairs without recombination rate estimates.