when I checked my paired-end RNAseq data, I saw some weird result. Figure is here
basically two genome features have same coordinate(as highlighted in red), however, their fpkm value is different. I wonder anyone have some ideas why this occur?
By the way, I am using Tophat v2.0.4, Cufflinks v2.0.2 and cummeRbund v2.0.0.