Pipeline for detecting (TF) Chip-seq peaks in transposable elements?

Question

[Biojl]

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

[Sinji]

Could give RepEnrich a try.

[Biojl]

I am interested in particular copies, not family enrichment. Therefore I want to call peaks at specific locations.

Answer 1

[miller.uthscsa]

I have been looking for one for a while, but I don't think it really exists yet. I know the Hammell lab is working on one called TEpeaks (https://github.com/yingjin07/TEpeaks). Also there was a recent study which did this using a custom pipeline https://www.nature.com/articles/s41467-018-08006-y