During my RNA-seq assembly, I found many misassemble or SNP or indel in UTR region.
I used SOAPdenovo-trans, Trinity and others.
They always generated lots of redundancy.
And this redundancy generated from UTR regions even though the gene body have well consensus sequence.
Cause of this UTR difference, I think they generated a lot of redundancy.
Do you have any idea of this happening?
I think the coverage of UTR is lower than gene body.
Please give me some reference.