New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Signal values for 0 CNV region #93
Comments
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?
—
Reply to this email directly, view it on GitHub
<#93>, or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ABNG3OHSBCWWHO32PVSFPR3WD3LH5ANCNFSM6AAAAAARIJVKBE>
.
You are receiving this because you are subscribed to this thread.Message
ID: ***@***.***>
|
-Does the file name need to have *.txt in suffix? What if just signalfile? |
the txt suffix is not required |
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) visualize.cnv.pl --format plot --signal 2.5Mv1.1.3998646007_R01C01 filename.rawcnv --snpposfile filename xyz |
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?
The text was updated successfully, but these errors were encountered: