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Old 04-27-2012, 03:04 AM   #2
Location: Cambridge area, UK

Join Date: Jan 2010
Posts: 35

hi antu82,

I would suggest you to give a look at CNAnorm (here the paper that describe it) We developed it to analyse low coverage data and we usually run up to 20 samples per GAIIX lane using tags. A milion mapped reads give you a decent resolution (comparable to aCGH)

As a reference, we usually use a pool of reads from the 1000 genome project, divided by gender (a pool of males and a pool of females).

if the tumour is not heterogeneous, you should also be able to get the absolute ploidy, especially if you have a rought estimate of tumour content.
stefanoberri is offline   Reply With Quote