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Old 02-20-2018, 06:22 AM   #1
azibat
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Location: Germany

Join Date: Mar 2013
Posts: 3
Default Error FishingCNV_2.1

Hello everybody,
hope, someone has a solution for the following problem:

I want to establish FishingCNV for analysis of CNVs in exomic data. All the pipeline runs good so far unless the last step. When typing

Code:
Rscript FishingCNV.R -c controls.ctr.complete -v -s ./sample.rpkm  -o ./ -pca
I get the following warnings and execution is halted:

Quote:
Error occured in plotting function. Program will proceed without the offending plot.
Execution halted.
R is properly installed (v3.2.3) as is the DNAcopy package.
The problem seems to be something with the sample file.

Has anbody have an idea?

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Old 02-21-2018, 02:38 AM   #2
azibat
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Location: Germany

Join Date: Mar 2013
Posts: 3
Question

Hello everybody,
I figured out what the problem was. Maybe it will be interesting to others:

The plotting command halted due to too low sample number in pooled control.rpkm. The problem was the control, not the sample.

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cnv calling, fishingcnv

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