I'm new in bioinformatics and not so familiar with RNA-Seq Data. So I have a very simple question about your RNA-Seq Data. For example, I have download the long polya+ RNA-Seq data from ENCODEenter link description here. It's in the view of Genes Gencode V7 and contains more than 50000 genes' expression level information (RPKM). I find that there are so many genes' expression level in 0. However, I'm confused about whether they are expressed or not. They may indeed not be expressed. Or they may be expressed a lot in polya-RNA or microRNA type and we don't extract them from a polya+ extraction. I think this problem is also remained in transcripts data. So I don't know how to use the ploya+ RNA-Seq data to identify the gene's expression level (about level 0 genes).
So who can give me a help? And thank you very much!