closest TSS of given peaks

[lewewoo]

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!

[Dario1984]

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

[lewewoo]

Thanks!
I will try it for sure!

[crazyhottommy]

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.

[gene_x]

bedtools?

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

[kadircaner]

you can also use GREAT - great.stanford.edu

[ashuchawla]

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

[crazyhottommy]

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

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