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Hi I have a list of ChipSeq peaks, what are the fastest way to find the closest TSS in the given length (for example, 1kb, 2kb... 10kb); Any tools or Perl scripts for this? Thanks a lot!
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There is a Bioconductor package called ChIPpeakAnno. If you know the R language, you should use it. -
Thanks!
I will try it for sure!Comment
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or you can use http://cistrome.org/ap/
based on Galaxy.
under the cistrome tool box
go to Integrative Analysis, click peak2gene: Peak Center Annotation
you can get a list of genes close to your peaks.Comment
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you can also use GREAT - great.stanford.eduComment
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I have to do it the other-way round - I have to find the peaks near all the genes in Human. I have the peak list with start and end positions. I also have a gene list with start transcription and end transcription .
Any pointers on how to do that would be really appreciated
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as suggested, have a try for bedtools http://bedtools.readthedocs.org/en/l...s/closest.html
Originally posted by ashuchawla View PostI have to do it the other-way round - I have to find the peaks near all the genes in Human. I have the peak list with start and end positions. I also have a gene list with start transcription and end transcription .
Any pointers on how to do that would be really appreciatedComment
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