Will submit to Galaxy my additions.
Thanks
Vasu
--- On Wed, 7/6/11, Jeremy Goecks <[email protected]> wrote:
From: Jeremy Goecks <[email protected]>
Subject: Re: [galaxy-user] Looking for new transcripts with cufflinks
To: "vasu punj" <[email protected]>
Cc: "GavinOliver" <[email protected]>, "David Matthews"
<[email protected]>, "galaxy-user" <[email protected]>
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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