I asked a similar question through "Contact Us", and I saw one question blow asked for a list of "primary_transcripts", i.e. one representative gene model per locus. My question is: Is there a way to find out which isoforms have in general the highest expression (FPKM etc) through all RNAseq results? I think the most abundant isoforms are better representatives than isoforms with the longest ORF.
If you don't have such data yet, can we assume the isoforms ending with ".1" as the representatives? TAIR10 had a set of "representative_gene_models", and their IDs not necessarily end with ".1". I am curious how the isoforms were numbered in Araport11.
<em>No answers yet</em>