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Question: Need help with "VCF-BEDintersect:" tool
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gravatar for blc2688
4.0 years ago by
blc2688 • 0
United States
blc2688 • 0 wrote:

I'm trying to look at RNApolII ChIPseq data from a mouse using the rat genome as the reference.  I want to know what genetic structures the peaks are closest to (e.g. regulatory regions, exons, introns, etc.). Is this the right tool to use?  What is a VCF dataset?  And where would I acquire one for a rat? 

 

Tool name: VCF-BEDintersect:
Tool version: 0.0.2
Tool ID: toolshed.g2.bx.psu.edu/repos/anton/vcfbedintersect/vcfbedintersect/0.0.2
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/anton/vcfbedintersect

 
vcf-bedintersect: • 927 views
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modified 4.0 years ago by rjcmrodrigues • 0 • written 4.0 years ago by blc2688 • 0
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gravatar for rjcmrodrigues
4.0 years ago by
rjcmrodrigues • 0
Germany
rjcmrodrigues • 0 wrote:

VCF is a Variant Calling File (http://vcftools.sourceforge.net/) it's basically for SNP analysis. I really don't think that's what you are looking for.
ADD COMMENT • link written 4.0 years ago by rjcmrodrigues • 0
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