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Old 03-18-2013, 05:05 PM   #1
lewewoo
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Default 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!
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Old 03-18-2013, 09:00 PM   #2
Dario1984
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There is a Bioconductor package called ChIPpeakAnno. If you know the R language, you should use it.
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Old 03-19-2013, 06:20 AM   #3
lewewoo
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Thanks!
I will try it for sure!
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Old 03-19-2013, 08:00 AM   #4
crazyhottommy
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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.
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Old 03-19-2013, 09:07 AM   #5
gene_x
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bedtools?

see: http://bedtools.readthedocs.org/en/l...s/closest.html
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Old 03-20-2013, 12:33 PM   #6
kadircaner
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you can also use GREAT - great.stanford.edu
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Old 06-27-2013, 01:05 PM   #7
ashuchawla
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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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Old 06-27-2013, 01:20 PM   #8
crazyhottommy
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as suggested, have a try for bedtools http://bedtools.readthedocs.org/en/l...s/closest.html


Quote:
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
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