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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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visualize_cnv.pl #89

Open psychrb opened 2 years ago

psychrb commented 2 years ago

1) Is is possible that a row that appears in the my raw.cnv file would not appear in visualize_cnv.pl output? For example, When I enter visualize_cnv.pl -format plot -signal signal.txt myfile.rawcnv NOTICE: Signal values for 0 CNV region is found in signal.txt I get this error eventhough myfile.rawcnv has a row with this signal file, signal.txt and the marker Name/coordinates?? How can I resolve this ERROR/NOTICE, if I see the CNV call (Name/coordinates) for signal.txt in the raw.cnv file? 2) Also can the raw.cnv file that is used for visualize_cnv.pl be the cnv file that is output after clean_cnv.pl or should it only be the raw.cnv file generated initially?

kaichop commented 2 years ago

The file name needs to be exactly identical in the ex.rawcnv file as signal.txt. Sometimes users have path name in the file name and this causes problem. Additionally, you may check whether the markers for the CNV in ex.rawcnv indeed exist in signal.txt file (sometimes it is not the case).

On Fri, Aug 19, 2022 at 7:37 PM psychrb @.***> wrote:

Is is possible that a row that appears in the raw.cnv file would still not appear in visualize_cnv.pl? For example, When I enter visualize_cnv.pl -format plot -signal signal.txt ex.rawcnv NOTICE: Signal values for 0 CNV region is found in signal.txt I get this error eventhough ex.rawcnv has a row with this signal file, signal.txt?? How can I resolve this ERROR/NOTICE, if I see the CNV call if the raw.cnv file?

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psychrb commented 2 years ago

Is it OK if the matching file name in raw.cnv file and the signal.txt file name has punctuation for example, "2.5Mv1.1.3998646158_R07C01" or "1M.5511192140_R01C02"? Could this specific file name or its format contribute to this error? Thank You.

kaichop commented 2 years ago

This is marker name, not file name. It should not matter if there is a dot or underline in the marker name. If you print out a few lines of ex.rawcnv, you will see that file name is one of the columns.

On Thu, Aug 25, 2022 at 10:33 AM psychrb @.***> wrote:

OK if the file name in raw.cnv file and the signal.txt file name has punctuation for example, "2.5Mv1.1.3998646158_R07C01" or "1M.5511192140_R01C02". Thank You.

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psychrb commented 2 years ago

I checked both of these issues. (1) The file name in .rawcnv file is same file name as signal.txt and (2) the markers in the raw.cnv file are in the SNP position file. But I still get the same error, "NOTICE: Signal values for 0 CNV region is found in the signal.txt file.. -Should all CNVs in the raw.cnv file (each row) be visualizable?? -Any other suggestions to resolve this? I can see the row with the CNV call in raw.cnv for this signal.txt file. Thanks.

kaichop commented 1 year ago

I skipped this issue earlier. There is no specific format restrictions/limitations to the name of the signal.txt file, but it must be identical as the name in .rawcnv file. (something like "folder1/signal.txt" in rawcnv will be not be recognized as the same as the signal.txt file.

On Fri, Oct 7, 2022 at 11:48 PM psychrb @.***> wrote:

Are there format restrictions or limitations to name of the signal.txt file?

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