cufflinks counts vs. rsem counts

[papori]

Hi all!
i have reference transcriptome with 76,000 contigs that ware built with trinity(DeNovo) from my experiment.
Next, i wanted to know counts per contig.
I started with rsem and i got table of 76,000 contigs with count per contig.
When trying to get count table with cufflinks i got table of 42,000 contigs.
How can it be?
Cufflinks dosent refer to some contigs in purpose?
Any ideas?

Thanks

[mfawzy]

This post is very old, but I am going to reply for others to benefit from my answer,

The result you got for cufflinks makes sense, since, cufflinks perform abundance estimation by two steps, the first step is a transcript assembly then the second step will be quantitation or abundance estimation, so i think, cufflinks assembled some of these contigs into larger contigs, this is why the number of contigs outputted from cufflinks is lesser than from rsem,