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-bounces@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.Matthews@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.
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Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034.
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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.Matthews@bristol.ac.uk wrote:
From: David Matthews D.A.Matthews@bristol.ac.uk Subject: Re: [galaxy-user] Looking for new transcripts with cufflinks To: "Oliver, Gavin" gavin.oliver@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-bounces@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.Matthews@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
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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.
Will submit to Galaxy my additions. Thanks Vasu
--- On Wed, 7/6/11, Jeremy Goecks jeremy.goecks@emory.edu wrote:
From: Jeremy Goecks jeremy.goecks@emory.edu 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/%C2%A0or send them to us.
Best, J.
galaxy-user@lists.galaxyproject.org
-
David Matthews -
Jeremy Goecks -
vasu punj