One idea is to look at the cufflinks output isoforms.fpkm_tracking. This would list an FPKM for each isoform, and you could add up the FPKM for all the isoforms which include the 3'UTR to estimate the FPKM of the region.

Thank you very much for helpful comment. I will try that. Actually, I use basespace on Illmina cloud, is it possible to open file the fpkm files?

Sorry I can't see anything relevant in the Basespace help files. You could download the bam files and run cufflinks yourself, or maybe check this by contacting Basespace Help in person?

One more question. How can I open the fpkm file? Download the driver??

Thanks Dr. Moore! I would contact to Illumina.

I am not familiar with Basespace, however, if you can get the bam file, you can easily get the interested region. If you are interested in particular exon, then you can use DEXSeq on the bam file to get result on differential expression of exon (http://bioconductor.org/packages/release/bioc/html/DEXSeq.html). However, if you are interested in a small region, e.g. just the 3'UTR of the particular gene, then you can simply make a gtf file containing information of only that region, then you can get the raw count using HTSeq or you can use cufflink providing your own gtf file to get the FPKM value if you want.

Thanks for helpful comments! I will check raw data on the cufflinks again.

Thanks again!