Question about Cufflinks Log Output

[adumitri]

Hi,

I was wondering if anyone could help me interpret the following part of Cufflinks' output:

> Map Properties:
>       Normalized Map Mass: 284238.81
>       Raw Map Mass: 284238.81
>       Fragment Length Distribution: Empirical (learned)
>                     Estimated Mean: 190.09
>                  Estimated Std Dev: 77.77
[12:23:09] Assembling transcripts and estimating abundances.

Do the Estimated Mean and Estimated Std Dev values refer to the insert size?
Our analyses involve paired-end, 100 ntd-long reads, and the values we calculated for (5 million reads of each of) our samples using bowtie2 and Picard tools are somewhat lower than the ones we get in the Cufflinks log. Consequently, I wanted to find out if the difference is something to worry about, or if it is just a consequence of not using the whole samples when estimating the insert size measures.

Thank you!
Alexandra