cuffdiff output files are empty

[pinki999]

Hi,

I downloaded the new version of cufflinks and tried to use cuffdiff. I just used the -N option for upper quartile normalization and my output files are empty. I got the following warning messages

[09:52:55] Modeling fragment count overdispersion.
Warning: fragment count variances between replicates are all zero, reverting to Poisson model
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
> Map Properties:
> Upper Quartile: 93.00
> Read Type: 50bp single-end
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80


And this was repeated quite a number of times with different upper quartile values.

Note: I am using the .gtf file downloaded from ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/ (for the hg18 build)

Thank you

[byb121]

Could you post the command line that you use? Also the whole process should be started from cufflinks, then cuffmerge/cuffcompare, then at last to cuffdiff.