I have results of targeted sequencing. It is several csv files (tables) with information about the identification number of amplicon (in two samples there are equal number of amplicons - 202) and amplicon coverage (number of reads which "cover" amplicon). 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, PCA, clustering analysis and so on...), but I don't quite sure what will be statistically correct?
*important moment: inside sample there is kind of competition for reagents, so if one amplicon will be "covered" by reads more then others will be "covered" less.