Question: Pipeline for detecting (TF) Chip-seq peaks in transposable elements?
gravatar for Biojl
2.2 years ago by
Biojl1.6k wrote:


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:

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

ADD COMMENTlink written 2.2 years ago by Biojl1.6k

Could give RepEnrich a try.

ADD REPLYlink written 2.2 years ago by Sinji2.8k

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

ADD REPLYlink written 2.1 years ago by Biojl1.6k
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