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ChIP-Seq: PAVIS: a tool for Peak Annotation and Visualization. Newsbot! Literature Watch 0 09-07-2013 08:20 AM

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Old 07-22-2015, 02:39 AM   #1
sbcn
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Default ChIP-seq annotation bidirectional promoters: any tool?

Hi all,

I am annotating peaks from a ChIP-seq experiment.

The problem I face is that some of the peaks fall on bidirectional promoters.

I would like to be able to get an output annotation that gives me information about the nearest TSS on the + strand AND on the - strand, and not only selecting the closest one, regardless of the strand.

I don't think HOMER can do this (correct me if I'm wrong), and also tried ChIPpeakAnno and ChIPseeker but I would like to know if there is a tool that could be advised in that context?

Thanks a lot!
Sarah
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