Cufflinks, without GFF-error

Question

[milady81]

Dear All Biostars:)

Me and my colleague are working with RNA-seq data and each of us got the same problem, using cufflinks.

First what I did:

tophat2 without gff file (because if I used the gff file, the cufflinks was taking and calculating the FPKM for genome-genes_corrdinates.gff without short reads mapped there.

and after I tried to run the cufflinks like that:

cufflinks -p 8 -o cufflinks accepted_hits.bam

and I got NOTHING.

You are using Cufflinks v2.2.1, which is the most recent release.
[12:07:28] Inspecting reads and determining fragment length distribution.

> Processed 1 loci.                            [*************************] 100%
> Map Properties:
>    Normalized Map Mass: 68.00
>    Raw Map Mass: 68.00
>    Fragment Length Distribution: Truncated Gaussian (default)
>                  Default Mean: 200
>               Default Std Dev: 80
[12:07:28] Assembling transcripts and estimating abundances.

> Processed 0 loci.                            [*************************] 100%

I tried to find the solution here in biostar.org and also on other website but what I only found was that maybe we don't have enough RAM but for sure we have enough. We are using big server.

Could someone help me (us)? What is wrong and how to solve the problem?

I am running out of time and still I don't know how to run the cufflinks to get the results:)

Cheers
Dorota