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Question: CpG Sites // CG dinucleotides
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gravatar for ibetfer3
15 months ago by
ibetfer3 • 0
ibetfer3 • 0 wrote:

Hello, I would like to know how to get the CpG sites (not islands) from a region of interest. Can anybody help me? Thank you very much!
cg dinucleotides cpg sites cpg • 422 views
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modified 15 months ago by Jennifer Hillman Jackson ♦ 25k • written 15 months ago by ibetfer3 • 0
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gravatar for Jennifer Hillman Jackson
15 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you have a VCF dataset with variant calls, the tool VCFfilter could be used.

If you have a BAM dataset of mapped reads, the tool DeepTools: computeGCBias could be used.

If you have genome coordinates and want to find out known CpG sites, examine the tracks at UCSC (http://genome.ucsc.edu) or your data source of choice. Once the data is loaded to Galaxy, filter it by region. Which tool to use for filtering depends on that data's format.

Reference Galaxy tutorials: https://galaxyproject.org/learn/

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 15 months ago • written 15 months ago by Jennifer Hillman Jackson ♦ 25k
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