How does cuffdiff/cufflinks determine "read type"?

[sdarko]

From a recent cuffdiff run:

> Map Properties:
>	Total Map Mass: 5798099.00
>	Number of Multi-Reads: 0 (with 0 total hits)
>	Read Type: 106bp x 106bp
>	Fragment Length Distribution: Empirical (learned)
>	              Estimated Mean: 171.87
>	           Estimated Std Dev: 55.64
> Map Properties:
>	Total Map Mass: 5795202.00
>	Number of Multi-Reads: 0 (with 0 total hits)
>	Read Type: 105bp x 105bp
>	Fragment Length Distribution: Empirical (learned)
>	              Estimated Mean: 171.90
>	           Estimated Std Dev: 55.69

These are from 100bp x 100bp reads, why would cufflinks believe that they are 105bp or 106bp paired-end reads?

[fabrice]

I have the same problem. I used cufflinks 1.0.3.

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: 366.70
> Read Type: 108bp x 102bp
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80

[fabrice]

I cannot understand why there is this warning. I have trimed my data, is this the reason?

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.

[Balat]

I also get the same warning. I am also using trimmed reads. Can any one explain why cufflinks thinks that the reads are single end even though the bam file was produced using paired reads in tophat?