This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Genomic variability R

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.

genome r chip-seq gene
• 2,100 views • link
updated by Chris Fields Chris Fields • written by mzezza • mzezza

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

• 0 views • link
written by ddiez ddiez

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.

• 0 views • link
written by mzezza • mzezza

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

• 0 views • link
written by ddiez ddiez

Yes! Extactly! Can you help me ?

• 0 views • link
written by mzezza • mzezza

1 answer

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!

• 0 views • link
written by Chris Fields Chris Fields

Log in to answer this question.

More posts like this