Retrotransposon analysis on ChIP-seq data.

Question

[SP]

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

Answer 1

[Gary]

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.