[galaxy-user] Cuffmerge - "Use Sequence" option.

Hi, Can anyone shed light on what the "use sequence" parameter (Y/N) in Cuffmerge is doing? The Cuffflinks manual says: -s/--ref-sequence <seq_dir>/<seq_fasta> This argument should point to the genomic DNA sequences for the reference. When "no" is chosen for the "use sequence" option I still get genomic coordinates for each entry. Also, when "no" is chosen, I get less entries than when "yes" is chosen. Any insight would be greatly appreciated. Have a great day. Cheers, Mo Heydarian