Cuffmerge: merging reference and transcript GTFs?

[mra]

Dear All.

After running cufflinks

cufflinks -p 10 --frag-len-mean 400 --frag-len-std-dev 100 -N --GTF-guide ${gtf} --frag-bias-correct ${fasta} --multi-read-correct -o cufflinks_all all.accepted_hits.bam

I got a 12M transcripts.gtf file that I eventually merged with a 240M reference GTF file using cuffmerge:

cuffmerge -p 10 -o cuffmerge_all --ref-gtf ${gtf} --ref-sequence ${fasta} assemblies.txt

(on assemblies.txt there is only the transcripts.gtf produced previously by cufflinks)

Yet, cuffmerge outputs a 142M merged.gtf. Assuming that cuffmerge makes a non-redudant union of the transcripts and reference GTF files, shouldn't merged.gtf weight at least as the reference GTF (240M)?

Thanks in advance