How Do I Compare Sequence Quality/Coverage Between Two Species?

Question

[pld]

I am looking at SLC5A5 in humans, but in rhesus I am seeing what might be poor sequence coverage in that region. I am interested in seeing if the gene is really truncated, or if there are potential lapses in coverage in the genomic sequence. Is there a way to check this visually with UCSC genome browser? Or is there another tool I can use?

Answer 1

[Emily]

If you mean the rhesus macaque Macaca mulatta then you can see the coverage quite nicely in Ensembl. Here you can see that there are gaps in the blue contig, indicating gaps in the assembly. To see how this might affect the gene, take a look at the region comparison view, choosing human as your species to compare to. Here you can see that some of the assembly gaps correspond to exons of the human gene, suggesting why the macaque model may be truncated.

[pld]

Rhesus is the common name of Macaca mulatta (and sometimes Japanese macaques), not the common name of members of Macaca. Eg Macaca fascicularis is commonly called a Cynomolgus or Cyno for short. Not to be pedantic, but it is an important distinction.

Thanks for the solution, this is exactly what I was hoping for.

[Emily]

I thought it was the right species, but wasn't certain if the name sometimes referred to other species - when in doubt, go for latin.