I am new to galaxy as well as RNA seq analysis. Although, I did not perform RNA seq, I am trying to follow that same pipeline to analyze my RIP-seq data. In brief, I extract RNAs from IPs and I am interested in finding the mRNA transcripts. My sequences are already aligned to the reference genome. It there a way for me to perform PCA to see the overlap of transcripts between samples? The PCA I have done somehow just overlaps the samples but I am interested in overlapping the transcripts to see how similar the transcripts are in different samples. Thanks in advance!