Will submit to Galaxy my additions. Thanks Vasu Subject: Re: [galaxy-user] Looking for new transcripts with cufflinks To: "vasu punj" <punjv@yahoo.com> Cc: "GavinOliver" <gavin.oliver@almacgroup.com>, "David Matthews" <d.a.matthews@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.