Genomic variability R

Question

[mzezza]

Hi,

I would have the need to have a quantitive information relatively to the genetic variability between two chromosomal regions of two or more human genomes.

I've tried with some R packages like ChIPpeakAnno and ChIPseeker without results.

Can I get some advice ?

Thanks and sorry for my imperfect english.

[ddiez]

It is unclear to me what you mean by genetic variability. Are you looking for SNPs? (then unclear why using ChIP).

[mzezza]

Thanks for answer. No, I'm not looking for SNPs. I need to understand if the chromosomal region of interest, in comparison, is a highly variable region or not. I need a mere quantitative data.

[ddiez]

So you want to compare two chromosomal regions and tell whether they are similar or not? Like performing sequence alignment?

[mzezza]

Yes! Extactly! Can you help me ?

Answer 1

[Chris Fields]

If you are comparing alignments and read coverage I suggest using deepTools. We use it quite frequently to run correlation analyses across samples and generate basic heatmaps, etc. It's quite nice!