Cufflinks cannot detect some transcripts without -g ref.gtf

[CHLin]

After I handled fastq files from Illumina pair-end strand-specific RNA-seq by Bowtie and Tophat and Cufflinks, I found the Cufflinks cannot detect some of the transcript even if there were some mapped reads (just like in the fig).

I wonder it might result from the low FPKM, but there're some defined transcript with lower FPKM...

Does anyone have the same problem or have the solution?

Thanks