cufflinks: Only one transcript per gene

Question

[GouthamAtla]

When I used cufflinks on bam file from tophat2, I got only one transcript per gene in the transcripts.gtf file for most of the samples. Has any one encountered this before? My data is illumina 100bp PE.

[GouthamAtla]

I realised that each sample has only one transcript per gene but the transcripts are different across different samples. Hence, if I use cuffmerge, I would get genes with multiple transcripts. In my case 29000 genes and 32000 transcripts after using cuffmerge.