Hi,

Anyone knows a good pipeline to call TFBS peaks using chip-seq data in transposable elements? Most of the traditional pipelines rely on uniquely mapped reads, and obviously there are a depletion of peaks in TEs as a consequence.

I've located two potential softwares for the alignment part:

• CSEM: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002111
• AREM: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216101/

I was wondering if someone has more up-to-date recommendations and other softwares for other parts of the pipeline (i.e. is macs2 a good option?)

Thanks in advance