FPKM minimum and maximum values ?

[repinementer]

I successfully ran cufflinks and my gene.expr and transcripts.gtf and others are showing FPKM values. Maximum I observed in my data is 444467 FPKM and minimum is <0.

Are my values are in correct range ?

Cufflinks paper results figure show FPKM ranges from 10 -100.

ANy suggestions ?

[GKM]

There is no way you could get negative FPKMs.

My suspicion is that the 444467 is either mitochondrial or ribosomal, or something of that sort, and the library may not even be polyA selected, but some sort of Ribo-depleted.

If you provide these details, it would be helpful

Anway, you may want to mask those regions when you run cufflinks, as they affect quantification of everything else, and if they aren't uniform across samples, they will affect any between-samples comparisons too.

[repinementer]

Yes you are right. There are no negative values. The least i observed was 0. And the library was rRNA depleted one.
May I know the usual range of FPKM values people get ? And also where could I get the below mask.gtf file (Annotated rRNA and mitochondrial transcripts?)
I will run again cufflinks by using -M mask.gtf file and will let you know.