I've got a naive question for you, and I would really appreciate your thoughts.
I found some transposable elements (TE) that were differentially expressed in a certain tissue, based on a case-control analysis of RNA-seq data using DESeq2, and a custom-made annotation for TEs. Now, I would like to investigate whether those differentially expressed TEs are expressed in a different tissue, for which I've already obtained raw TE counts in 20 control samples. In this part of my analysis, all samples are part of the same group, so I am not sure how to go on to obtain normalised read counts, to then establish a "basal expression cut-off" and calculate the overlap with TEs differentially expressed in my previous analysis. How do I do this? How do I calculate this overlap? (Would this be a simple overlapping test (e.g., R package "GeneOverlap"), or some hypergeometric probability?)
I found R libraries like TissueEnrich which allow me to match genes of interest to publicly available data, but the TE expression I am interested is not on these databases.