Hello Bodour,
If the genome you are using as at UCSC, then yes, the BED and Interval
files will have a link to UCSC, but the wig files will not by default.
To view the wig data, you can use the Galaxy Track browser or IGB
directly, or convert the file to bigWig and then view it at UCSC with
the tool "Convert Formats -> Wig/BedGraph-to-bigWig".
The "PEAKS" bed file is the primary output of the tool. The other data
files are supporting evidence or alternate views. Bringing up all the
data together in a browser would be a good way to understand how they
fit together.
View the original MACS documentation:
http://liulab.dfci.harvard.edu/MACS/00README.html
And tutorials including MACS are here:
- https://main.g2.bx.psu.edu/u/james/p/exercise-chip-seq
- https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
(protocol 3)
- http://wiki.galaxyproject.org/Learn#Other_Tutorials -> Analysis of
ChIP-seq data in Galaxy
Hopefully this helps,
Jen
Galaxy team
On 2/20/13 8:33 AM, Bodour Al-Khamees wrote:
Hello,
I am using the Galaxy web tool to analyze ChIP-seq data. By applying
MACS algorithm, the Galaxy browser generated bed and wig files. Within
the Galaxy browser, the bed file has a link to the UCSC Genome browser
whereas the wig file has no link to the UCSC browser. I wonder which
file is best to visualize the peaks in the UCSC Genome browser and how?
Any experience or just thoughts?
Thank you very much in advance!
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___________________________________________________________
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:
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