Will submit to Galaxy my additions.
Thanks
Vasu

--- On Wed, 7/6/11, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:


From: Jeremy Goecks <jeremy.goe...@emory.edu>
Subject: Re: [galaxy-user] Looking for new transcripts with cufflinks
To: "vasu punj" <pu...@yahoo.com>
Cc: "GavinOliver" <gavin.oli...@almacgroup.com>, "David Matthews" 
<d.a.matth...@bristol.ac.uk>, "galaxy-user" <galaxy-user@lists.bx.psu.edu>
Date: Wednesday, July 6, 2011, 10:08 AM











One question related to this If I am intrested in annotated genes/transcripts, 
what change I may have to make in command line while runnig Cufflinks so that 
it will give both unknown as well as known transcrpts and genes?
Thanks


You probably want the -g/--GTF-guide parameter; from the Cufflinks 
documentation:


--
Tells Cufflinks to use the supplied reference annotation (GFF) to guide RABT 
assembly. Reference transcripts will be tiled with faux-reads to provide 
additional information in assembly. Output will include all reference 
transcripts as well as any novel genes and isoforms that are assembled.
--


This isn't currently implemented in Galaxy's Cufflinks but probably will be in 
the future. As always, community contributions are most welcome; if you've 
implemented something in your Cufflinks/compare/diff Galaxy wrappers that isn't 
available in the Galaxy repository, please submit them to the Community 
site: http://community.g2.bx.psu.edu/ or send them to us.


Best,
J.
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