Understanding patterns of diversity in the pseudoautosomal region
The PAR_Project is a study that computes the nucleotide diversity along the X chromosome of 26 unrelated females in order to look at the diversity differences between the recombining and non-recombinging regions.
There are two pseudoautosomal regions (PARs) on the sex chromosomes that recombine during male meiosis. The PAR1 is approximately 2.7 Mb and the PAR2 is approximately 320kb on the tips of the sex chromosomes.
It is expected that due to the recombination, the PARs will have a higher nucleotide diversity. In this study, we look at the PAR boundary, which is thought to be due to an inversion of the XG gene that spans the PAR boundary. We use the nucleotide diversity to see if there is a strict boundary between the recombining and non-recombining regions. The mutation rate is controlled by normalizing the human data with data from the chimpanzee and the rhesus macaque.
In this study, we also look at the diversity in the X-transposed region (XTR), which is human specific and according to a recent study is thought to be a third PAR.
This folder, Shared_codes, contatins the basic scripts and the initial data. Not all Galaxy intervals are included. These programs are all pointed toward a specific directroy for I/O and the ~ directory should be set for your computer.