[BioC] Different number of genes when using HTseq and cuffdiff

[Fatemehsadat Seyednasrollah]

Hi,

 I have used the same output tophat bam files both for HTseq (and then DESeq) and cuffdiff to find DE genes. But  I do not understand why even when the bam files and references are the same the number of genes are different in the result of cuffdiff and HTseq. Actually I expected to have different number of counts for each gene but not getting more (nearly 100) number of genes in HTseq comparing to cuffdiff. 
Thank you in advance