Initial look at total data
Here is an initial look at the total data set. First of all, I looked at median read depth. I am disappointed that the median read depth for my newest set of libraries seems so low (green), despite the PCR duplicate rate also being low. Don't quite understand what is going on. Maybe we get fewer reads out of HiseqX lanes when doing duplex barcode sequencing? Also looked at IBS and super clone assignment. Here is the corrplot: Sequenced a good many As. In total, we sequenced 83 super clone individuals. 30 B super clone individuals, and 26 super clone C individuals (D10 clones, bottom right corner in figure above). For designating super clone assignment, I did two things. First of all, I looked at the distances in the IBS matrix between single moms and pooled moms for the 6 clones where I did libraries using both approaches. Most of the 6 grouped together tightly, but one set had an identity of 0.945. I then looked at a histogram of identity distances: You can see ...