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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