problem with gffread and exon_number

[jake13]

I ran cufflinks to find novel transcripts on my RNA-seq samples and want to run cuffdiff. However, I want to first filter out any novel single exon transcripts before running cuffmerge. I have been using the following command:

gffread transcripts.gtf -g $gencode_fasta -FUTE -o transcripts_multiexon_full.gtf

However, in the initial transcripts.gtf file each transcript lists the field exon_number "#". However, this information seems to be lost when I run gffread. Is there some other option that I am missing to keep this information? Is there a better way to do this?
Thanks