Conserved genes' exon missing and/or split

Question

[nr]

Hi All,

I have a question regarding conserved gene split and exons missing from the conserved genes.

When you compare two genome assemblies of the SAME SPECIES but with different kmer sizes (For example, one genome assembly built with kmer size 71 and another genome assembly built with kmer size 61), why would exons of conserved genes be missing and fragmented in one genome assembly but present and complete in another genome assembly?

Regards, Niraj

Answer 1

[h.mon]

Because one assembly is more fragmented than the other. There are many sources to read, like this old thread here on Biostars, and even the Wikipedia k-mer entry discusses assembly and k-mer size. The Bandage wiki has nice graphics showing the effects of k-mer size on assembly.