Question: ExomeDepth package- error with "select.reference.set" function
0
gravatar for Bouzid.a
10 weeks ago by
Bouzid.a0
Bouzid.a0 wrote:

Hello,

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
1

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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