Question: Is cn.mops can be used for detecting CNV for targeted sequencing of 8M region
0
gravatar for iszhucy
23 months ago by
iszhucy0
iszhucy0 wrote:

Hi,

I wanna check whether cn.mops is appropriate for a ~8M region of targeted sequencing.

I wanna call CNV for hybrid capture sequencing data of one contiguous targeted region (~8M), but have no idea whether cn.mops is suitable.

I have 19 cases (not tumor) and 2 controls (not match normal).  For cn.mops, "recommend to useat least 6 samples for proper parameter estimation."  In this case, can I still use cn.mops to call CNV? or any additional matters to be noticed?

Thanks in advance!

cn.mops • 391 views
ADD COMMENTlink modified 23 months ago by Günter Klambauer540 • written 23 months ago by iszhucy0
Answer: Is cn.mops can be used for detecting CNV for targeted sequencing of 8M region
0
gravatar for Günter Klambauer
23 months ago by
Austria
Günter Klambauer540 wrote:

Hello,

Yes, certainly you can cn.mops for that. You might want to use our newly developed "panelcn.mops" that has been optimized for targeted sequencing data: http://www.bioinf.jku.at/software/panelcnmops/  (Paper, Github, Implementation,...)

Regards,

Günter

 

ADD COMMENTlink written 23 months ago by Günter Klambauer540

Hi, Günter

Thanks for your suggestion.

Actually, I noticed panelcn.mops at the same time.  The manual said "recommend to use at least eight high quality samples as controls samples; if more control samples are used, the results typically become more robust."  But I have only 2 controls, is this OK?  

Additionally, the panelcn.mops seems to be designed for NGS panel data.  Just to check again, my data is one contiguous region about 8M in one chromosome, not genes from multiple locations.  In this case, is there anything special to do before using panelcn.mops?

Thanks a lot!

ADD REPLYlink written 23 months ago by iszhucy0

Hello,

For good performance you would need eight high quality samples, but if you only have 2 then you can still try it out -- after all, it is the best thing you can do and the alternative would be to not analyse the data. Note, that the performance estimates that we give in our paper will not hold in this case and you should find a way to estimate sensitivity and specificity on your data. Maybe you have some ground truth (known copy numbers) in your data? Or maybe you can find or put together a similar data set from a public source?

panelcn.mops also works in your case of one contiguous region. No, I think you can use panelcn.mops without workaround.

For more information please contact the first author of the panelcn.mops paper or the according bioconductor support site.

Thanks for your interest!

ADD REPLYlink written 23 months ago by Günter Klambauer540

Hi, Günter

Thanks a lot for your suggestions, which are really helpful for me.

ADD REPLYlink written 23 months ago by iszhucy0
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