We have received 454 targeted sequencing data (low depth) and would like to identify copy number segments from this. The rep at 454 said that read depth in this case might not be the most indicative of deletions or amplifications.
I was wondering what the best way to go about this would be? Are there programs that will identify segments from such data? Or, is there a graphical way to look at certain regions? We have CGH data that identified some segments and we would like to validate them using our 454 data.
Any help would be greatly appreciated!