I would like to define a bedfile for chromosome X, to target only basepairs outside of pseudo-autosomal regions (and going forward other regions, too).
First, I wasn't able to find an already prepared bedfile in any of the online repositories (but let me know if it is available somewhere).
Second, I compiled the bedfile for all basepairs in chromosome X as a starting point (by looking at the latest assembly at genome browser):
chrX 0 156040895 # as defined at https://genome.ucsc.edu/
The genome browser is 1-based and the last base is inclusive, while the bedfile is 0-based and last base is not inclusive, therefore I had to subtract 1 from the bed
Afterwards, I wanted to exclude the pseudo-autosomal regions as defined at this page. However, I am not sure if basepair "Start" and "Stop" are 0- or 1-based and inclusive/not inclusive. I might use the same convention used on the genome browser, but I am not sure if that's correct in this case. I wasn't able to find this information on their website or online.
Assuming that the NCBI "Start" and "Stop" field follow the UCSC parameters (1-based and inclusive), the resulting bed (PAR regions excluded) might be the following:
chrX 0 10000 chrX 2781479 155701382
Edit: the section on the centromeres has the "Length" parameter, from which I could infer that "Start" and "Stop" base-pairs are both inclusive. At the same time, the "Stop" base-pair of PAR#2 in chromosome X is base-pair 156,030,895, which is also the last base-pair number if we were considering the UCSC genome browser notation (1-based and inclusive). Therefore, it seems to me clear that the same notation is used, and the proposed bed-file should be correct.