Entering edit mode
2.4 years ago
Toby
▴
10
Hi,
I'm trying to map the recombination events / synteny that have occured around my chromosomes of the reference genome, a really good assembly with full length chromosomes. If I dotplot my chromosome / regions of the chromosome I can see some really large scale similarity >100kb in some instances. I've been trying to find a tool that can map these for me, ideally just output the coordinates of similiarity or something I can at least process to that effect.
The tools I've seen seem to either be for populations and detecting against a reference or don't seem to be able to compile, which makes me think I'm missing something.
Thanks,
Toby
are you comparing your genome assembly with a related species to find synteny? or are you looking at self-self alignments? might help get better answers with those details
Self-self alignments between chromosomes to identify shared regions. With these sequences coming from the reference
possibly you could look into calling "segdups" (segmental duplications) in your assembly. that may help with the "translocation" aspect of your interest. I am less familiar with the recombination aspect. maybe having haplotype-specific assemblies would help with that?