problem about StringTie expression

[kentnf]

The StringTie could output expression on both gene-level (with -A parameter) and transcript-level (t_data.ctab).
The total FPKM value of gene is ~1,000,000; but the total FPKM value of transcript is just ~600,000.
For the same sample and reference GTF, the total FPKM of transcript is ~2,400,000 using cufflinks to compute the expression.

The expression show big difference between Cufflinks and StringTie. Which one is correct?

[kentnf]

Find another problem for StringTie on detecting the expression of lncRNAs. One of my interesting lncRNA is a single-exon transcript, part of this lncRNA overlapped with gene region. I know this lncRNA should highly expressed in specific samples. Using cufflinks, we could detect the expression of this lncRNA for those specific samples. But using StringTie, the lncRNA express value is 0 on several of those specific samples.