Question: Retrotransposon analysis on ChIP-seq data.
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gravatar for SP
3.8 years ago by
SP250
Germany
SP250 wrote:

I want to analyse my ChIP-seq data for retrotransposons binding sites, Can somebody suggest me any tool which can be used for that? And how does pair end or single end sequencing effect the analysis?

Thanks   

chip-seq • 1.0k views
ADD COMMENTlink modified 3.8 years ago by Gary450 • written 3.8 years ago by SP250
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gravatar for Gary
3.8 years ago by
Gary450
Taiwan/Taichung/China Medical University Hospital
Gary450 wrote:

LTR_FINDER (Xu & Wang, 2007) could be one of options. In addition, one related paper (Chuong, et al, 2013) for your information.

Xu, Z. & H. Wang (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res., 35, W265.

Chuong, E. B., M. A. K. Rumi, M. J. Soares & J. C. Baker (2013) Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nature Genetics, 45, 325.

ADD COMMENTlink written 3.8 years ago by Gary450
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