Question: Coverage profile comparison
gravatar for faramer86
5 months ago by
faramer860 wrote:


I have results of targeted sequencing. It is several csv files  with information about amplicons (unique id of amplicon and number of reads). It looks like that (*image below). And I have to compare two coverage profiles of two samples. There are several methods to do that (Pearson correlation, Euclidean distance, Chi-square, t-test, clustering analysis and so on...), but I don't quite sure what will be statistically correct?

The goal is to validate the result. I have two samples (control and new) and I want to know that the coverage profile of new sample is the same with control sample.

*important moment: inside sample there is kind of competition for reagents, so if one amplicon will be "covered" high-covered then others will be "covered" less.



ADD COMMENTlink modified 5 months ago • written 5 months ago by faramer860

Not an answer but a suggestion: it sounds like you could fit a localised regression to the data and then compare coverage profiles that way. By doing this, you could also introduce covariates into the model. I have never done this previously; so, remains a suggestion.

ADD REPLYlink written 5 months ago by Kevin Blighe40

Thanks, Kevin! I will try this! And what do you think about correlation or chi-square? Is it statistically correct to use them in this case?

ADD REPLYlink written 5 months ago by faramer860

I think that the localised regression idea will stand better in a publication or report. You could fit the model and then check the coefficient to show that there are no differences between the 2 samples.

A correlation with a highly statistically significant p-value could assist, too. I am not sure about the use of a Chi Square test.

ADD REPLYlink written 5 months ago by Kevin Blighe40
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