Unpaired CNV Exome
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@nikhilgadewal-8562
Last seen 6.2 years ago
United States

I am working with cn.mops for CNV identification from exome data for unpaired samples.

The problem I am facing is, when I used "unpaired" mode, the zero  column in Readcounts matrix, but I use sampe samples with paired mode, normalization is done and no error.

I have attached the screenshot of the error. I have referred to the thread at biostar https://www.biostars.org/p/103494/

Any way to work with "unpaired" mode.

Thanks & regards,

-Nikhil

cn.mops • 669 views
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@gunter-klambauer-5426
Last seen 9 months ago
Austria

Hello Nikhil,

 

The "mode" argument does not refer to whether your samples are "paired" or "unpaired", but to the reads. If you have used a sequencing technology with paired end reads and used a read mapper that aligns paired reads, then your choice should be "paired". Otherwise the correct choice is "unpaired". 

This is also the reason why your read count matrix consist only of zeros when you pick the wrong option.

 

Regards,

Günter

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