Transcription Factor Binding sites intersecting Transposable Elements

Question

[M.Adiba]

Hi,

I am working with human RNA-Seq samples. From my analysis I ended up with a list of transcription factors. Now I want to-

1. find out the DNA binding sites of these TFs,
2. find out which of the Transposable elements from my annotation overlaps these DNA binding sites

the ultimate aim is to understand which TE elements can influence the binding of these TFs.

is there any tutorial that can help me with this? I did explore the MEME suite, generegulation by bioconductor, JASPER tools, but as I am new to this, some experienced suggestion will be really helpful.

Thanks in advance!