Question: Doubt about WL in cn.mops
gravatar for cased
17 months ago by
cased0 wrote:


I am Daniel Castillo Secilla, from University of Granada (Spain). I am using cn.mops for detecting CNVs but I have a question about how the paremeters WL (Windows Lentgh) works. When I used samples from the reference human genome hg19 I used a WL very low (5000) because I was trying different sizes, and the resultant plot was right, but then, I tried the same with samples from the current reference genome hg38 and, with this WL the plot has a lot of artifacts as you can see in grch38 with Artifacts image in the link below. So, I setted the WL with the value by default again (25000) and the artifacts of the plot were removed as you can see at figure grch38 without Artifacts image in the link below.

So I don't understand why these artifacts appear when the WL is too small and I hope that you can bring me some light in this situation. 

grch38 with Artifacts --> 

grch38 without Artifacts -->

I am looking forward to hearing from you.

Best regards.

dnaseq dnacopy cn.mops cnv genomic • 344 views
ADD COMMENTlink modified 17 months ago by Günter Klambauer540 • written 17 months ago by cased0

see below

ADD REPLYlink modified 17 months ago • written 17 months ago by Günter Klambauer540
Answer: Doubt about WL in cn.mops
gravatar for Günter Klambauer
17 months ago by
Günter Klambauer540 wrote:


This is an intrinsic problem of the read count data. If you have a small WL, the counts are low and you will easily get large fold-changes: Imagine that most samples of a readcount of 1 and one sample has a read count of 2. Then this would be a strong signal in terms of fold-changes (2-fold change).

Therefore, I suggest both in the paper and the manual to adjust the WL such that on average 100 reads are in a window. This depends of course on your coverage. The function "getReadCountsFromBAM" suggests and appropriate window length if you leave out that parameter.


ADD COMMENTlink written 17 months ago by Günter Klambauer540

Hi  Mr. Günter:

This information is very useful for me. Thank you very much for your quickly response! I understand your explanation and now I can continue my research without this doubt.

Best regards.


ADD REPLYlink written 17 months ago by cased0
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