Chip-Seq, Encode Peaks And Galaxy

Question: Chip-Seq, Encode Peaks And Galaxy

7.5 years ago by

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. 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

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modified 7.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.5 years ago by Radhouane Aniba • 40

7.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/

ADD COMMENT • link written 7.4 years ago by Jennifer Hillman Jackson ♦ 25k

Please keep me on the loop as I am also interested in similar workflow. Many thanks and best regards, Jorge

ADD REPLY • link written 7.4 years ago by Jorge Andrade • 20

Thanks Jennifer Rad 2011/6/23 Jorge Andrade <andrade.jorge@gmail.com> -- *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*

ADD REPLY • link written 7.4 years ago by Radhouane Aniba • 40

7.2 years ago by

Daniel Blankenberg ♦♦ 1.7k

United States

Daniel Blankenberg ♦♦ 1.7k wrote:

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

ADD COMMENT • link written 7.2 years ago by Daniel Blankenberg ♦♦ 1.7k

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