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  • closest TSS of given peaks

    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!

  • #2
    There is a Bioconductor package called ChIPpeakAnno. If you know the R language, you should use it.

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    • #3
      Thanks!
      I will try it for sure!

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      • #4
        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.

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        • #5
          bedtools?

          see: http://bedtools.readthedocs.org/en/l...s/closest.html

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          • #6
            you can also use GREAT - great.stanford.edu

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            • #7
              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

              Comment


              • #8
                as suggested, have a try for bedtools http://bedtools.readthedocs.org/en/l...s/closest.html


                Originally posted by ashuchawla View Post
                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

                Comment

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