Dear Michael, We're interested in identifying CNVs from a single exome dataset (data is Illumina paired-end, and there are no controls). Reading through the document of your tool exomeCopy, it seemed to me that exomeCopy can theoretically work on a single sample, but I'm still a little unsure about how the background read-depth would be estimated in that case, and whether or not it'd be meaningful. Can you please help clarify this? Thanks, Guru. -- Guru Ananda Computational Sciences Group The Jackson Laboratory 600 Main St, Bar Harbor ME 04609, USA Ph: 207-288-6290 Science is a way of thinking much more than it is a body of knowledge. (Carl Sagan) The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. [[alternative HTML version deleted]]

Hi Guru, It is possible to run exomeCopy without any calculated background read depth, using the GC content variables and the 'width' variable supplied to the X.names argument of exomeCopy(). Even better would be if you could find a few samples of "healthy" exomes which used the same enrichment kit as your dataset. By generating background from publicly downloaded exomes (we used ~10 from this dataset http://www.nature.com/ng/journal/v42/n11/full/ng.680.html ), we were more sensitive to detect duplications and deletions. Mike On Fri, Apr 26, 2013 at 6:24 PM, Guru Ananda <guru.ananda@jax.org> wrote: > Dear Michael, > > We're interested in identifying CNVs from a single exome dataset (data > is Illumina paired-end, and there are no controls). Reading through the > document of your tool exomeCopy, it seemed to me that exomeCopy can > theoretically work on a single sample, but I'm still a little unsure about > how the background read-depth would be estimated in that case, and whether > or not it'd be meaningful. Can you please help clarify this? > > Thanks, > Guru. > -- > Guru Ananda > Computational Sciences Group > The Jackson Laboratory > 600 Main St, Bar Harbor > ME 04609, USA > Ph: 207-288-6290 > > Science is a way of thinking much more than it is a body of knowledge. > (Carl Sagan) > > The information in this email, including attachments, may be confidential > and is intended solely for the addressee(s). If you believe you received > this email by mistake, please notify the sender by return email as soon as > possible. > [[alternative HTML version deleted]]