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