Cuffcompare Result help

[Wei-HD]

Dear all,

I just run cuffcompare -r [reference.GTF] [transcript.GTF], the output file included the transcripts.tmap which showed gene names and FPKM info. Following is one of the genes:

Bdnf ENSMUST00000053317 = CUFF.114250 CUFF.114250.1 97 32.073177 28.162251 35.984103 35.033306 1633 CUFF.114250.1
Bdnf ENSMUST00000111050 = CUFF.114251 CUFF.114251.2 100 33.063804 27.584704 38.542903 36.115361 1249 CUFF.114250.1
Bdnf ENSMUST00000111052 = CUFF.114252 CUFF.114252.3 62 20.483324 14.448689 26.517959 22.373791 1105 CUFF.114250.1
Bdnf ENSMUST00000111047 c CUFF.114254 CUFF.114254.1 100 10.649808 7.099872 14.199745 11.639716 235 CUFF.114254.1
Bdnf ENSMUST00000111042 c CUFF.114256 CUFF.114256.1 100 23.582192 21.902030 25.262353 25.777043 2323 CUFF.114256.1
Bdnf ENSMUST00000053317 p CUFF.114258 CUFF.114258.1 100 0.557202 0.000000 1.467470 0.609143 187 CUFF.114258.1

I am a bit confused with the result, since I have done qPCR experiment of BDNF gene, and it will be upregulated like 5-6 folds compared with control. I only run with the treated sample and the reference GTF file, so the FPKM value is not the like fold change, right? also the class code, should I only trust "="? and what does "p" and "i" mean? If I only use "=" FPKM value, how can I extract the one with the class code "="?

And if I run cuffcompare -r [reference.GTF] [treated.GTF] [control.GTF], how could I get the fold changes (treated/control)?

Sorry for such naive questions? Can someone kindly explain to me?

With many thanks in advance!!

Wei