RAD map v1

Last week I mapped the RAD sequences back to the oak contigs. After clustering the contigs, there are 3327 unique contigs, of which 23 were removed because they either don't have a map position or map to two positions > 3 cM distant. So we now have 803 RAD loci mapped to 587 Quercus robur contigs... that's a lot farther along than we were two weeks ago. To do the first four days this week:

• Quantify divergence between any two groups of individuals defined on the tree for mapped loci
• Plot divergence on this map
• Relate this map to the Q. rubra map
• Start analyzing the fuller set of RADs on the Morton server
• work with Isabella on mapping the larger contigs... status?

Then Jeanne comes on Thursday to start working together on the Q. rubra / Q. robur map.