cuffdiff- no assembled transcripts

[crh]

Hi

We are running tophat pipeline on algal sequences and our cuffdiff output does not appear to have assembled transcripts listed, rather CDS that correlate w/ single exons only.

tophat:
tophat2 -o ./psr1_rep_s2 -i 50 -I 28000 --min-segment-intron 50 --max-segment-intron 12800 -G Creinhardtii_236_gene_exons.gtf $BOWTIE_INDEX/bowtie2/cre5.3 psr1_p_replete_s2.fastqsanger.gz

cufflinks:
cufflinks -o ./cufflinks_out_psr1_rep_s2 -I 50000 -N –g Creinhardtii_236_gene_exons.gtf tophat_out_psr1_rep_s2/accepted_hits.bam

cuffdiff:
cuffdiff -o ./cuffdiff_out -L 1690_rep,psr1_rep,1690_dep,psr1_dep /merged_asm/merged.gtf list of accepted_hits.bam


example cuffdiff which returns tests for DE for each exon, but not entire transcript:
XLOC_000003 XLOC_000003 PAC:27578295.CDS.1 chromosome_1:20355-20687
XLOC_000004 XLOC_000004 PAC:27578295.CDS.2 chromosome_1:20759-21065
XLOC_000005 XLOC_000005 PAC:27578295.CDS.3 chromosome_1:21137-21443
XLOC_000006 XLOC_000006 PAC:27578295.CDS.4 chromosome_1:21513-21819
XLOC_000007 XLOC_000007 PAC:27578295.CDS.5 chromosome_1:21986-22132
XLOC_000008 XLOC_000008 PAC:27578295.CDS.6 chromosome_1:22453-22699
XLOC_000009 XLOC_000009 PAC:27578295.exon.7 chromosome_1:22862-22948
XLOC_000010 XLOC_000010 PAC:27578295.exon.8 chromosome_1:23106-23250
XLOC_000011 XLOC_000011 PAC:27578295.exon.9 chromosome_1:23370-23957


What am I missing besides the obvious?

thanks

Charles