From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a
Hi everyone, I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications. pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks. Is there someone who can point me to a step by step to do things to start using Galaxy ? Thank you Rad
Hello Rad, Dan will be able to help you get started and build up a workflow for your analysis. He is currently on vacation, but will be returning soon and will contact you directly when he returns. We are very sorry about the delayed reply. Please know that we definitely want to help you to use Galaxy for your project, We will be in touch, Best, Jen Galaxy team On 6/17/11 10:55 AM, Radhouane Aniba wrote:
Hi everyone,
I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications.
From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks.
Is there someone who can point me to a step by step to do things to start using Galaxy ?
Thank you
Rad
___________________________________________________________ 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/
Please keep me on the loop as I am also interested in similar workflow. Many thanks and best regards, Jorge On Thu, Jun 23, 2011 at 3:21 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello Rad,
Dan will be able to help you get started and build up a workflow for your analysis. He is currently on vacation, but will be returning soon and will contact you directly when he returns.
We are very sorry about the delayed reply. Please know that we definitely want to help you to use Galaxy for your project,
We will be in touch,
Best,
Jen Galaxy team
On 6/17/11 10:55 AM, Radhouane Aniba wrote:
Hi everyone,
I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications.
From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks.
Is there someone who can point me to a step by step to do things to start using Galaxy ?
Thank you
Rad
______________________________**_____________________________ 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<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/ ______________________________**_____________________________ 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<http://lists.bx.psu.edu/listinfo/galaxy-dev>
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Thanks Jennifer Rad 2011/6/23 Jorge Andrade <andrade.jorge@gmail.com>
Please keep me on the loop as I am also interested in similar workflow. Many thanks and best regards, Jorge
On Thu, Jun 23, 2011 at 3:21 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello Rad,
Dan will be able to help you get started and build up a workflow for your analysis. He is currently on vacation, but will be returning soon and will contact you directly when he returns.
We are very sorry about the delayed reply. Please know that we definitely want to help you to use Galaxy for your project,
We will be in touch,
Best,
Jen Galaxy team
On 6/17/11 10:55 AM, Radhouane Aniba wrote:
Hi everyone,
I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications.
From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks.
Is there someone who can point me to a step by step to do things to start using Galaxy ?
Thank you
Rad
______________________________**_____________________________ 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<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/ ______________________________**_____________________________ 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<http://lists.bx.psu.edu/listinfo/galaxy-dev>
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- *Radhouane Aniba* *Bioinformatics Postdoctoral Research Scientist* *Institute for Advanced Computer Studies Center for Bioinformatics and Computational Biology* *(CBCB)* *University of Maryland, College Park MD 20742*
Hi Rad, Jorge, Sorry for the delay in reply. We have not yet released a pre-canned workflow to do this. However, if you are looking to associate one set of Genomic interval/region data with another set, Galaxy's interval operation tools are a good place to begin. There are good examples of using these tools available through screencasts (http://galaxycast.org), Galaxy 101 (http://usegalaxy.org/galaxy101), as well as the wiki (http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations). Please let us know if we can provide additional information. Thanks for using Galaxy, Dan On Jun 23, 2011, at 9:41 AM, Radhouane Aniba wrote:
Thanks Jennifer
Rad
2011/6/23 Jorge Andrade <andrade.jorge@gmail.com> Please keep me on the loop as I am also interested in similar workflow. Many thanks and best regards, Jorge
On Thu, Jun 23, 2011 at 3:21 AM, Jennifer Jackson <jen@bx.psu.edu> wrote: Hello Rad,
Dan will be able to help you get started and build up a workflow for your analysis. He is currently on vacation, but will be returning soon and will contact you directly when he returns.
We are very sorry about the delayed reply. Please know that we definitely want to help you to use Galaxy for your project,
We will be in touch,
Best,
Jen Galaxy team
On 6/17/11 10:55 AM, Radhouane Aniba wrote: Hi everyone,
I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications.
From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks.
Is there someone who can point me to a step by step to do things to start using Galaxy ?
Thank you
Rad
___________________________________________________________ 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/ ___________________________________________________________ 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:
-- Radhouane Aniba Bioinformatics Postdoctoral Research Scientist Institute for Advanced Computer Studies Center for Bioinformatics and Computational Biology (CBCB) University of Maryland, College Park MD 20742
___________________________________________________________ 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:
participants (4)
-
Daniel Blankenberg -
Jennifer Jackson -
Jorge Andrade -
Radhouane Aniba