Coverage profile comparison
0
0
Entering edit mode
faramer86 • 0
@faramer86-17844
Last seen 3.6 years ago

Hello!

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.

image: https://drive.google.com/file/d/1o78wnJgVKs3QEUEZbSD4oTpdr7k5_zCw/view?usp=sharing

 

Targeted sequencing correlation coverage euclid clustering • 580 views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 422 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6