Cufflinks de novo assembly, single transcript per gene

Question

[rnaseq99]

I'm attempting to perform de novo transcriptome assembly using cufflinks. I have a single aligned rna seq bam file which I supply to cufflinks (without the -g option). I get the expected transcripts.gtf file output, but every gene id has only a single transcript associated with it, whereas I was expecting multiple transcripts per gene id. Have I done something wrong or is this the expected output of cufflinks?

[Mehmet]

Why are you using cufflinks for de novo assembly? By using Cufflinks, you should add a reference transcriptome with your transcriptome. If I remember correctly, Cufflinks tool is used for reference-based assembly.

You can use Trinity for de novo assembly.