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
--- On Mon, 7/4/11, David Matthews <d.a.matth...@bristol.ac.uk> wrote: From: David Matthews <d.a.matth...@bristol.ac.uk> Subject: Re: [galaxy-user] Looking for new transcripts with cufflinks To: "Oliver, Gavin" <gavin.oli...@almacgroup.com> Cc: "galaxy-user" <galaxy-user@lists.bx.psu.edu> Date: Monday, July 4, 2011, 2:15 PM Of course - Doh! Many thanks!! On 4 Jul 2011, at 18:47, Oliver, Gavin wrote: > "u" represents unknown intergenic transcripts. > > > -----Original Message----- > From: galaxy-user-boun...@lists.bx.psu.edu on behalf of David Matthews > Sent: Mon 04/07/2011 17:48 > To: galaxy-user@lists.bx.psu.edu > Subject: [galaxy-user] Looking for new transcripts with cufflinks > > Hi, > > I am working with HeLa cells and want to know how to get cufflinks etc. to > highlight if a region of the genome is being transcribed that is not in the > ensembl gtf. I know that cufflinks highlights with class code "j" regions > that do not match a known gene and therefore may be novel but most of these > arise from transcription on or near known genes. Does anyone know how to look > for transcription that is clearly distinct from known genes? This is a wild > goose chase but worth a peek just in case... > > > Best Wishes, > David. > > __________________________________ > Dr David A. Matthews > > Senior Lecturer in Virology > Room E49 > Department of Cellular and Molecular Medicine, > School of Medical Sciences > University Walk, > University of Bristol > Bristol. > BS8 1TD > U.K. > > Tel. +44 117 3312058 > Fax. +44 117 3312091 > > d.a.matth...@bristol.ac.uk > > > > > > The contents of this message and any attachments to it are confidential and > may be legally privileged. If you have received this message in error, you > should delete it from your system immediately and advise the sender. > > Almac Group (UK) Limited, registered no. NI061368. Almac Sciences Limited, > registered no. NI041550. Almac Discovery Limited, registered no. NI046249. > Almac Pharma Services Limited, registered no. NI045055. Almac Clinical > Services Limited, registered no. NI041905. Almac Clinical Technologies > Limited, registered no. NI061202. Almac Diagnostics Limited, registered no. > NI043067. All preceding companies are registered in Northern Ireland with a > registered office address of Almac House, 20 Seagoe Industrial Estate, > Craigavon, BT63 5QD, UK. > > Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034. > > Almac Clinical Services LLC, Almac Clinical Technologies LLC and Almac > Diagnostics LLC are Delaware limited liability companies and Almac Group > Incorporated is a Delaware Corporation. More information on the Almac Group > can be found on the Almac website: www.almacgroup.com > ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
