Hi,
Any idea when the server is going to be up again?
Boaz
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] on behalf of Joachim Jacob | VIB | [joachim.jacob@vib.be] Sent: Friday, September 06, 2013 10:32 AM To: kanwarjag@gmail.com Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] Bam QC and coverage
Hi Shamsher,
Another alternative is to use bamqc from the qualimap suite. The wrapper you can find at: http://toolshed.g2.bx.psu.edu/view/joachim-jacob/qualimap_suite
You need to install this tool in a local Galaxy, with the qualimap suite installed and perl (see README).
Cheers, Joachim
On 09/04/2013 09:59 PM, shamsher jagat wrote:
I am looking for a tool to perform QC of Bam file especially following functions:
- BAsic information and stat.
- Coverage across reference features- gene/ transcripts.
Is it possible to do it in Galaxy? Thanks
-- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
___________________________________________________________ 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:
To search Galaxy mailing lists use the unified search at:
Co-ask : When will the Galaxy Server work again?
Thanks for Galaxy Team's work and support!
On Mon, Sep 9, 2013 at 5:03 AM, Boaz Shaanan bshaanan@bgu.ac.il wrote:
Hi,
Any idea when the server is going to be up again?
BoazBoaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710
From: galaxy-user-bounces@lists.bx.psu.edu [ galaxy-user-bounces@lists.bx.psu.edu] on behalf of Joachim Jacob | VIB | [ joachim.jacob@vib.be] Sent: Friday, September 06, 2013 10:32 AM To: kanwarjag@gmail.com Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] Bam QC and coverage
Hi Shamsher,
Another alternative is to use bamqc from the qualimap suite. The wrapper you can find at: http://toolshed.g2.bx.psu.edu/view/joachim-jacob/qualimap_suite
You need to install this tool in a local Galaxy, with the qualimap suite installed and perl (see README).
Cheers, Joachim
On 09/04/2013 09:59 PM, shamsher jagat wrote:
I am looking for a tool to perform QC of Bam file especially following functions:
- BAsic information and stat.
- Coverage across reference features- gene/ transcripts.
Is it possible to do it in Galaxy? Thanks
-- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
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:
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
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:
To search Galaxy mailing lists use the unified search at:
Hello Boaz,
The public Main Galaxy server experienced issues leading to unexpected downtime over the weekend. These have since been resolved. Please let us know if problems persist.
Our apologies for the inconvenience,
Jen Galaxy team
On 9/9/13 2:03 AM, Boaz Shaanan wrote:
Hi,
Any idea when the server is going to be up again?
BoazBoaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710
From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] on behalf of Joachim Jacob | VIB | [joachim.jacob@vib.be] Sent: Friday, September 06, 2013 10:32 AM To: kanwarjag@gmail.com Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] Bam QC and coverage
Hi Shamsher,
Another alternative is to use bamqc from the qualimap suite. The wrapper you can find at: http://toolshed.g2.bx.psu.edu/view/joachim-jacob/qualimap_suite
You need to install this tool in a local Galaxy, with the qualimap suite installed and perl (see README).
Cheers, Joachim
On 09/04/2013 09:59 PM, shamsher jagat wrote: I am looking for a tool to perform QC of Bam file especially following functions:
- BAsic information and stat.
- Coverage across reference features- gene/ transcripts.
Is it possible to do it in Galaxy? Thanks
-- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
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:
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
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:
To search Galaxy mailing lists use the unified search at:
Hello Ben,
The public Main Galaxy server experienced issues leading to unexpected downtime over the weekend. These have since been resolved. Please let us know if problems persist.
Our apologies for the inconvenience,
Jen Galaxy team
On 9/9/13 6:44 AM, Ben Ben wrote:
Co-ask : When will the Galaxy Server work again?
Thanks for Galaxy Team's work and support!
On Mon, Sep 9, 2013 at 5:03 AM, Boaz Shaanan <bshaanan@bgu.ac.il mailto:bshaanan@bgu.ac.il> wrote:
Hi, Any idea when the server is going to be up again? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il <mailto:bshaanan@bgu.ac.il> Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu <mailto:galaxy-user-bounces@lists.bx.psu.edu> [galaxy-user-bounces@lists.bx.psu.edu <mailto:galaxy-user-bounces@lists.bx.psu.edu>] on behalf of Joachim Jacob | VIB | [joachim.jacob@vib.be <mailto:joachim.jacob@vib.be>] Sent: Friday, September 06, 2013 10:32 AM To: kanwarjag@gmail.com <mailto:kanwarjag@gmail.com> Cc: galaxy-user@bx.psu.edu <mailto:galaxy-user@bx.psu.edu> Subject: Re: [galaxy-user] Bam QC and coverage Hi Shamsher, Another alternative is to use bamqc from the qualimap suite. The wrapper you can find at: http://toolshed.g2.bx.psu.edu/view/joachim-jacob/qualimap_suite You need to install this tool in a local Galaxy, with the qualimap suite installed and perl (see README). Cheers, Joachim > On 09/04/2013 09:59 PM, shamsher jagat wrote: > I am looking for a tool to perform QC of Bam file especially following > functions: > 1. BAsic information and stat. > 2. Coverage across reference features- gene/ transcripts. > Is it possible to do it in Galaxy? > Thanks -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org <http://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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org <http://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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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:
To search Galaxy mailing lists use the unified search at:
galaxy-user@lists.galaxyproject.org
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Ben Ben -
Boaz Shaanan -
Jennifer Jackson