How would you define homologous windows between 2 genomes?
Hello,
Let's say I have genome A and genome B, each of a single chromosome. How would you define homologous windows between the two?
What I can think of is 1) mapping with minimap2 the 2 chromosomes 2) look at the output to find homologous blocks in the paf file.
Does this sound like the correct approach? Now my problem is, what do I do if I want, say, windows of 10 Kb? How do I go from a PAF file to a bed file with 10 Kb windows that are homologous between genomes A and B. Any idea of the tools or approach?
Thanks
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to identify structural variants (SV) breakpoints using alignment PAF file?
written by BioinfoBee •
-
Reducing BWA mem seed length when a genome is highly heterozygous?
written by Axzd •
-
how can i filter a sam file from a paf file
written by Mark •
-
Reconstructing reference Info of CHM13 reads
written by Martin •
-
How extract read ID from a bam file per mapped feature (gene)
written by valopes •
-
Opinion about a genome comparisson pipeline.
written by K.Gee •
-
extracting unmapped reads from PAF file
written by Ric
-
Parser for PAF to find structural variants
written by crimsontabaq •
-
Minimap2 generated a very large paf, and miniasm failed to get gfa, how to do with it ?
written by lovenlong •
-
RNA-Seq analysis = only 10 DE genes
written by ste.lu
Depends what you are interested in, you could go by using a genome-genome alignment using Cactus (https://github.com/ComparativeGenomicsToolkit/cactus).
SatsumaSynteny may also be of interest, which is a k-mer based genome-genome alignment tool. If you're just looking at regions around genes, you could use an anchored synteny tool. I'm a little out of date with these, but something like MCScanX may be suitable.
Thanks! I think this will do