Question: Which is the right bin size for CNV detection in low pass WGS single cell?
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gravatar for am
13 months ago by
am20
European Union
am20 wrote:

Hello! I'm performing a single-cell genome-wide copy-number profiling by low-pass sequencing (coverage: 1X, 0.5X, 0.1X). Would anybody suggest me how to determine which is the optimal bin size in the genome segmentation step? Usually it's set to 0.5M or 1M when the genome coverage is as low as 1X. I would like to know which is the best one for my coverage, any advice? Thank you!

ADD COMMENTlink modified 13 months ago by Tomás Di Domenico30 • written 13 months ago by am20

Which tool are you using for the analysis?

ADD REPLYlink written 13 months ago by igor12k

I'm testing different tools such as CNVkit, Gingko, Control-FREEC... In the CNVkit manual for example I read: "Increase the “target” average bin size (--target-avg-size), e.g. to at least 1000 bases for 30x coverage, or proportionally more for lower-coverage sequencing". I would like to expand this concept.

ADD REPLYlink written 13 months ago by am20
1

I am not sure about the others, but Control-FREEC can automatically determine the optimal bin size.

ADD REPLYlink written 13 months ago by igor12k
2

I second the use of Control-FREEC. It is a truly great program suite, that can determine copy number from WGS, WES, or targeted seq.

ADD REPLYlink modified 13 months ago • written 13 months ago by Kevin Blighe71k

Thank you Igor and Kevin. Yes, the coefficientOfVariation parameter in Control-FREEC allows to automatically determine the correct window size.

ADD REPLYlink written 13 months ago by am20
1
gravatar for Tomás Di Domenico
13 months ago by
Madrid, Spain
Tomás Di Domenico30 wrote:

The first author of this paper has developed an interactive app that lets you play around with your sample characteristics and see how that would affect the required read depth to be able to perform CNV calling: https://gmacintyre.shinyapps.io/sWGS_power/

ADD COMMENTlink written 13 months ago by Tomás Di Domenico30

Bizarrely, they do not seem to have done any adjustment for GC content, which will affect coverage at different genomic regions. As such, on face value, this appears to be yet one more copy number program that is not addressing all of the issues.

ADD REPLYlink modified 13 months ago • written 13 months ago by Kevin Blighe71k

This is not a CNV program, just a tool to help you estimate the depth you need based on sample characteristics before you do your sequencing.

ADD REPLYlink modified 13 months ago • written 13 months ago by Tomás Di Domenico30

Gracias por la clarificación / Thanks for confirming.

ADD REPLYlink written 13 months ago by Kevin Blighe71k

The answer was not really for you, but rather so that other people don't just dismiss the tool because of your comment. I think it can indeed be useful.

Fantastic Spanish, by the way.

ADD REPLYlink written 13 months ago by Tomás Di Domenico30

De nada

ADD REPLYlink written 13 months ago by Kevin Blighe71k
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