I just found that Cufflinks2 is not the right software for me with respect of the output should contain the types of loci in genome (exons, introns, UTRs, and transposons), and the read numbers/levels in each locus;
Cufflinks2 only counts the expression levels in different genes(transcripts), rather than in all different genomic features;
Does anyone know whether BEDtools are the solution to this problem? And which BEDtool should I use?
I am keeping reading about BEDtools, but I will appreciate it if anyone can give any suggestions. Many thanks!