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Question: Clustering Algorithm In Galaxy
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gravatar for Daniel Elleder
6.8 years ago by
Daniel Elleder • 30
Czech Republic
Daniel Elleder • 30 wrote:
Is there a good read clustering algorithm available in Galaxy? Specifically for 454 and Ion Torrent reads. In the Galaxy e-mail archive I see mentions of dnaclust, but I cannot find it in the menus.
galaxy • 906 views
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modified 6.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.8 years ago by Daniel Elleder • 30
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gravatar for Jennifer Hillman Jackson
6.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Daniel, I see the mailing list question you are referring to. I am fairly certain that the user developed their own wrapper. I checked in the Tool Shed and didn't find a DNA Clust wrapper added. You could consider posting to galaxy-dev@bx.psu.edu to see if anyone or if that specific user has a galaxy wrapper for this tool that is ready for general use that could be added to the Tool Shed. Two other options, that are not really the same thing, but I'll mention them anyway, just in case they are useful: 1) Multiple Alignments -> ClustalW 2) After mapping (with any NGS mapper): NGS: SAM Tools -> BAM-to-SAM -> Convert SAM to interval then: Operate on Genomic Intervals -> Cluster the intervals of a dataset Best wishes for your project, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD COMMENT • link written 6.8 years ago by Jennifer Hillman Jackson ♦ 25k
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