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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Signal values for 0 CNV region #93

Open psychrb opened 1 year ago

psychrb commented 1 year ago

I'm trying to visualize a CNV from the raw.cnv file but get an error when running visualize_cnv.pl: 'Signal values for 0 CNV regions is found in signal.txt file'. I checked and the raw.cnv file contains the signal.txt file in one column (exact match) and the SNP position file matches the positions in signal intensity file. Any other tips/suggestions to resolve this?

kaichop commented 1 year ago

The name "signal.txt" must be exactly identical as the column in raw.cnv file (sometimes people have directory name in front of the file name and this causes problems). If they are indeed identical, you may just create a fake CNV that is say 200kb or 100 SNPs in size and then see if the signals can be plotted correctly. This helps diagnose the problem.

On Tue, Oct 18, 2022 at 1:14 PM psychrb @.***> wrote:

I'm trying to visualize a CNV from the raw.cnv file but get an error when running visualize_cnv.pl: 'Signal values for 0 CNV regions is found in signal.txt file'. I checked and the raw.cnv file contains the signal.txt file in one column (exact match) and the SNP position file matches the positions in signal intensity file. Any other tips/suggestions to resolve this?

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psychrb commented 1 year ago

-Does the file name need to have *.txt in suffix? What if just signalfile? -Do you mean as a test to create a 'fake' CNV in the raw.cnv file or the signal intensity file? Thanks.

kaichop commented 1 year ago

the txt suffix is not required fake CNV call in the raw.cnv file so that you can plot the signal values. you did not show the command or the LOG/ERROR message so I am not sure what is the problem.

psychrb commented 1 year ago

I still get the same error, when I enter in a 'fake CNV' in a rawcnv file. All SNP positions in snpposfile match the SNP positions in signal intensity file. No file path in column, just the file name (see first rows of rawncnv file below) Log of error is below. Please advise of workaround? In the example below: "2.5Mv1.1.3998646007_R01C01" is the signal intensity file

visualize.cnv.pl --format plot --signal 2.5Mv1.1.3998646007_R01C01 filename.rawcnv --snpposfile filename xyz NOTICE: Start reading snpposfile xyzposfile...Done with location information for 2372784 markers NOTICE: "Signal values for 0 CNV region is found in signal intensity file"