Cuffilinks 1.3.0 FPKM

[giuliano stirparo]

Hello everyone!

I am using a pipeline to analyze RNAseq data from solid 5500.
Firstly I aligned my reads with TopHat obtaining .bam files.
Now I am running Cufflinks 1.3.0.

I was wondering why I could not get any FPKM values different from zero when I use the annotation .gtf file.

I tried to run Cufflinks without any .gtf file and in this case I succeded in obtaining FPKM values.

Do you have any idea?

Thanks

[paolo.kunder]

I encountered the same problem still no solution...

[kopi-o]

Maybe you have different chromosome names in the GTF file and the BAM file. That's one common reason.

[Robby]

Try to download the gtf-reference from the Cufflinks-homepage. I had already a couple of times the same problem when using the reference from the UCSC-page.

[honey]

Gtf

It is an old issue add prefix Chr in column with chromoes numbers.