Mo,

Take a look at the Cuffmerge documentation: 
http://cufflinks.cbcb.umd.edu/manual.html#merger_input

Best,
J.

On Apr 26, 2012, at 3:39 PM, Mohammad Heydarian wrote:

> 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
> 
> 
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