Post Galaxy-ChIP-seq analysis: UCSC Genome browser can't read the wig file
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!
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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