I'm looking into performing some whole-genome alignments of several nonhuman primate species, but I'm a little confused about which sequences I should include or exclude. Here is my current list of things I'm not sure about?
- Some of the species that I plan to align do not have mitochondrial or Y-chromosome assemblies available, while others do. Is this likely to cause problems, or can I ignore it?
- If I include both X and Y chromosomes, do I need to mask the pseudo-autosomal region in one or the other?
- What should I do with unlocalized sequences (e.g. "chr1_gl000191_random", "chrUn_gl000211")? What about the "hap" sequences (e.g. "chr6_apd_hap1")?
(No, not all my species are on UCSC, so I can't just use their alignments. If only.)