I have pairs of transcripts that overlap on the genome, but I am not sure if they actually belong to the same gene or not. I have expression data for many different samples and I was thinking to perform a correlation test between each overlapping pair.
I can do cor.test() with method="spearman", but I guess maybe this is not the best for RNA-seq data? And also I need to correct for multiple testing.
Any suggestions on how to best perform this test? I want to remove all the gene pairs that are significantly correlated.