Question: CNV Profile figure
0
gravatar for tanbiswas6
8 months ago by
tanbiswas60
tanbiswas60 wrote:

Hi, I'm using Control-FREEC to identify CNVs. After installing I've used a sample data whose CNV profile looks like the figure below (link provided) where pink represents copy number gain and green represents loss. I don't how how to interpret this kind of CNV profile and what does each dots represents and why there is a line below just above the X-axis? Could anybody explain regarding this? https://ibb.co/VqDddf2

control-freec cnv • 250 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by tanbiswas60
1

Please see this post to add an image to your post. Please use imgbb, not Google Drive.

ADD REPLYlink written 8 months ago by RamRS30k

The job is not fully done yet. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

Please carefully read the post I linked to and use it well.

ADD REPLYlink written 8 months ago by RamRS30k

I have not worked with freec but for me your sample looks qc failed

ADD REPLYlink written 8 months ago by German.M.Demidov1.8k

Agreed, this looks crazy messy. What sort of data is this? Exome, wgs? I've never used Control-FREEC, but it doesn't look like segmentation is being performed either.

ADD REPLYlink written 8 months ago by jared.andrews077.1k

This WES data and ControlFC does segmentation itself. But still that data looks so noisy. That's why can't interpret it. I've used sorted BAM files (created using GATK best practice pipeline) as an input for ControlFC.

ADD REPLYlink written 8 months ago by tanbiswas60

Have you done QC on the WES data? This looks like a potential quality issue.

ADD REPLYlink written 8 months ago by jared.andrews077.1k
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