cummeRbund / cuffdiff output

[mkagan]

I aligned RNAseq reads and ran cuffmerge then cuffdiff on the transcripts.gtf file, with a mouse genome annotation from UCSC.

Everything works and seems correct.

When I analyze the results using CummeRbund, i get
CuffSet instance with:
2 samples
99458 genes
136223 isoforms
112151 TSS
24701 CDS
99458 promoters
112151 splicing
20273 relCDS


This is my first time working with mouse data, but why are there so many genes? This doesn't seem right. Should be like 17K genes ... Does anyone know what's going on?

There are a total of 6 samples here, that are grouped as two samples in cuffdiff.