Question: ExomeDepth package- error with "select.reference.set" function
gravatar for Bouzid.a
10 weeks ago by
Bouzid.a0 wrote:


For CNV detection from targeted NGS data, I'm running the ExomeDepth tutorial, but in the step of building the most appropriate reference set as following:

my.choice <- select.reference.set (test.counts = my.test,reference.counts = my.reference.set, bin.length = (my.counts.dafr$end - my.counts.dafr$start))

I received the following errors:

Optimization of the choice of aggregate reference set, this process can take some time It looks like the test samples has only 0 bins with 2 or more reads. The coverage is too small to perform any meaningful inference so no likelihood will be computed.

Any recommendation, please? Thanks for your help.

cnv exomedepth • 114 views
ADD COMMENTlink written 10 weeks ago by Bouzid.a0

Yeap, looks like your coverage is empty (0 bins) covered at least with one read. Some reading error.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by German.M.Demidov1.5k

Thanks for your reply. So, unfortunately, the ExomeDepth package will not be applicable to my data!!

ADD REPLYlink written 10 weeks ago by Bouzid.a0
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