Is there an option of running CEAS tool in Galaxy I want to annotate selected enriched regions of ChIP seq data with gene names etc?
Thanks
Hello,
This particular tool group from is not incorporated, but many similar components exist as tools in Galaxy. In particular, the "Operate on Genomic Intervals -> Profile Annotations for a set of genomic intervals" tool may be useful. If not, then importing a gene track (UCSC, ENSEMBL, etc.) and using the other operations in this tool group can bring together annotation features.
Hopefully this gives some options for your project,
Jen Galaxy team
On 11/8/11 1:58 PM, shamsher jagat wrote:
Is there an option of running CEAS tool in Galaxy I want to annotate selected enriched regions of ChIP seq data with gene names etc? Thanks
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:
Cistrome (instance of GALAXY) has CEAS included.
Ian
________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] on behalf of Jennifer Jackson [jen@bx.psu.edu] Sent: 08 November 2011 22:43 To: shamsher jagat Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] CEAS in Galaxy
Hello,
This particular tool group from is not incorporated, but many similar components exist as tools in Galaxy. In particular, the "Operate on Genomic Intervals -> Profile Annotations for a set of genomic intervals" tool may be useful. If not, then importing a gene track (UCSC, ENSEMBL, etc.) and using the other operations in this tool group can bring together annotation features.
Hopefully this gives some options for your project,
Jen Galaxy team
On 11/8/11 1:58 PM, shamsher jagat wrote:
Is there an option of running CEAS tool in Galaxy I want to annotate selected enriched regions of ChIP seq data with gene names etc? Thanks
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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___________________________________________________________ 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:
Thank you, Ian!
Shamsher, here is the link to the project: http://cistrome.org/
This is another instance of Galaxy, so a new registration/login will be required if you do not already have one for this site. http://galaxyproject.org/wiki/Public%20Galaxy%20Servers
Great!
Jen Galaxy team
On 11/9/11 4:25 AM, Ian Donaldson wrote:
Cistrome (instance of GALAXY) has CEAS included.
Ian
From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] on behalf of Jennifer Jackson [jen@bx.psu.edu] Sent: 08 November 2011 22:43 To: shamsher jagat Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] CEAS in Galaxy
Hello,
This particular tool group from is not incorporated, but many similar components exist as tools in Galaxy. In particular, the "Operate on Genomic Intervals -> Profile Annotations for a set of genomic intervals" tool may be useful. If not, then importing a gene track (UCSC, ENSEMBL, etc.) and using the other operations in this tool group can bring together annotation features.
Hopefully this gives some options for your project,
Jen Galaxy team
On 11/8/11 1:58 PM, shamsher jagat wrote:
Is there an option of running CEAS tool in Galaxy I want to annotate selected enriched regions of ChIP seq data with gene names etc? Thanks
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-devTo manage your subscriptions to this and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___________________________________________________________ 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:
galaxy-user@lists.galaxyproject.org
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Ian Donaldson -
Jennifer Jackson -
shamsher jagat