Visulization of raw 4C-seq reads in UCSC

Question

[amie.e.siemonek]

I'm trying to create bedGraph files to view raw and normalised reads from a 4C-seq experiment to view in UCSC for two biological replicates. Is there a simple way to do this?

I've tried using bamCoverage and expected to get peaks for read counts but instead I get long flat bars that look like stairs...I'm kind of unsure of how to determine what bin size to use or the appropriate method of normalization, which might explain the unusual results if anyone has any tips?

Answer 1

[Luis Nassar]

Hello,

If you send us a snippet of your data to our private mailing list ([e-mail]) we can take a look and suggest the best method for visualization.

Either a bedGraph or bigWig should work, but we may have to tweak some settings to optimize the resolution.